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 JMenuItem createSVG = new JMenuItem();
221 protected JMenuItem font = new JMenuItem();
223 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
225 JMenuItem epsFile = new JMenuItem();
227 JMenuItem LoadtreeMenuItem = new JMenuItem();
229 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
231 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
233 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
235 protected JMenuItem modifyPID = new JMenuItem();
237 protected JMenuItem modifyConservation = new JMenuItem();
239 protected JMenu sortByTreeMenu = new JMenu();
241 protected JMenu sort = new JMenu();
243 protected JMenu calculateTree = new JMenu();
245 JMenu jMenu2 = new JMenu();
247 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
249 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
251 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
253 protected ButtonGroup colours = new ButtonGroup();
255 JMenuItem vamsasStore = new JMenuItem();
257 protected JMenuItem showTranslation = new JMenuItem();
259 protected JMenuItem extractScores = new JMenuItem();
261 protected JMenuItem expandAlignment = new JMenuItem();
263 protected JMenu showProducts = new JMenu();
265 public JMenuItem openFeatureSettings = new JMenuItem();
267 JMenuItem fetchSequence = new JMenuItem();
269 JMenuItem annotationColour = new JMenuItem();
271 JMenuItem annotationColumn = new JMenuItem();
273 protected JMenuItem rnahelicesColour = new JMenuItem();
275 JMenuItem associatedData = new JMenuItem();
277 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
279 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
281 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
283 JMenu addSequenceMenu = new JMenu();
285 JMenuItem addFromFile = new JMenuItem();
287 JMenuItem addFromText = new JMenuItem();
289 JMenuItem addFromURL = new JMenuItem();
291 JMenuItem exportAnnotations = new JMenuItem();
293 JMenuItem exportFeatures = new JMenuItem();
295 protected JPanel statusPanel = new JPanel();
297 GridLayout gridLayout1 = new GridLayout();
299 JMenu jMenu3 = new JMenu();
301 JMenuItem showAllSeqs = new JMenuItem();
303 JMenuItem showAllColumns = new JMenuItem();
305 JMenu hideMenu = new JMenu();
307 JMenuItem hideSelSequences = new JMenuItem();
309 JMenuItem hideSelColumns = new JMenuItem();
311 JMenuItem hideAllButSelection = new JMenuItem();
313 JMenuItem hideAllSelection = new JMenuItem();
315 JMenuItem showAllhidden = new JMenuItem();
317 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
319 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
321 protected JMenuItem showAllAlAnnotations = new JMenuItem();
323 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
325 protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
327 protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
329 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
331 JMenuItem invertColSel = new JMenuItem();
333 protected JTabbedPane tabbedPane = new JTabbedPane();
335 JMenuItem save = new JMenuItem();
337 protected JMenuItem reload = new JMenuItem();
339 JMenuItem newView = new JMenuItem();
341 JMenuItem textColour = new JMenuItem();
343 JMenu formatMenu = new JMenu();
345 JMenu selectMenu = new JMenu();
347 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
349 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
351 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
353 protected JMenuItem gatherViews = new JMenuItem();
355 protected JMenuItem expandViews = new JMenuItem();
357 JMenuItem pageSetup = new JMenuItem();
359 JMenuItem alignmentProperties = new JMenuItem();
361 JMenu tooltipSettingsMenu = new JMenu();
363 private JMenuItem justifyLeftMenuItem = new JMenuItem();
365 private JMenuItem justifyRightMenuItem = new JMenuItem();
367 JMenu autoAnnMenu = new JMenu();
369 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
371 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
373 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
375 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
377 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
379 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
381 protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
383 protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
385 private JMenuItem grpsFromSelection = new JMenuItem();
387 private SequenceAnnotationOrder annotationSortOrder;
389 private boolean showAutoCalculatedAbove = false;
396 setJMenuBar(alignFrameMenuBar);
398 // dynamically fill save as menu with available formats
399 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
401 JMenuItem item = new JMenuItem(
402 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
404 item.addActionListener(new java.awt.event.ActionListener()
407 public void actionPerformed(ActionEvent e)
409 outputText_actionPerformed(e);
413 outputTextboxMenu.add(item);
415 } catch (Exception e)
417 System.err.println(e.toString());
420 if (!new jalview.util.Platform().isAMac())
422 closeMenuItem.setMnemonic('C');
423 outputTextboxMenu.setMnemonic('T');
424 undoMenuItem.setMnemonic('Z');
425 redoMenuItem.setMnemonic('0');
426 copy.setMnemonic('C');
427 cut.setMnemonic('U');
428 pasteMenu.setMnemonic('P');
429 reload.setMnemonic('R');
432 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
434 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
435 .getUserColourSchemes().keys();
437 while (userColours.hasMoreElements())
439 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
440 userColours.nextElement().toString());
441 radioItem.setName("USER_DEFINED");
442 radioItem.addMouseListener(new MouseAdapter()
445 public void mousePressed(MouseEvent evt)
447 if (evt.isControlDown()
448 || SwingUtilities.isRightMouseButton(evt))
450 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
452 int option = JOptionPane.showInternalConfirmDialog(
453 jalview.gui.Desktop.desktop,
455 .getString("label.remove_from_default_list"),
457 .getString("label.remove_user_defined_colour"),
458 JOptionPane.YES_NO_OPTION);
459 if (option == JOptionPane.YES_OPTION)
461 jalview.gui.UserDefinedColours
462 .removeColourFromDefaults(radioItem.getText());
463 colourMenu.remove(radioItem);
467 radioItem.addActionListener(new ActionListener()
470 public void actionPerformed(ActionEvent evt)
472 userDefinedColour_actionPerformed(evt);
479 radioItem.addActionListener(new ActionListener()
482 public void actionPerformed(ActionEvent evt)
484 userDefinedColour_actionPerformed(evt);
487 colourMenu.insert(radioItem, 15);
488 colours.add(radioItem);
491 colours.add(noColourmenuItem);
492 colours.add(clustalColour);
493 colours.add(zappoColour);
494 colours.add(taylorColour);
495 colours.add(hydrophobicityColour);
496 colours.add(helixColour);
497 colours.add(strandColour);
498 colours.add(turnColour);
499 colours.add(buriedColour);
500 colours.add(userDefinedColour);
501 colours.add(PIDColour);
502 colours.add(BLOSUM62Colour);
503 colours.add(nucleotideColour);
504 colours.add(purinePyrimidineColour);
505 // colours.add(covariationColour);
506 colours.add(tcoffeeColour);
507 colours.add(RNAInteractionColour);
508 setColourSelected(jalview.bin.Cache
509 .getDefault("DEFAULT_COLOUR", "None"));
513 public void setColourSelected(String defaultColour)
516 if (defaultColour != null)
518 int index = ColourSchemeProperty
519 .getColourIndexFromName(defaultColour);
523 case ColourSchemeProperty.CLUSTAL:
524 clustalColour.setSelected(true);
528 case ColourSchemeProperty.BLOSUM:
529 BLOSUM62Colour.setSelected(true);
533 case ColourSchemeProperty.PID:
534 PIDColour.setSelected(true);
538 case ColourSchemeProperty.ZAPPO:
539 zappoColour.setSelected(true);
543 case ColourSchemeProperty.TAYLOR:
544 taylorColour.setSelected(true);
547 case ColourSchemeProperty.HYDROPHOBIC:
548 hydrophobicityColour.setSelected(true);
552 case ColourSchemeProperty.HELIX:
553 helixColour.setSelected(true);
557 case ColourSchemeProperty.STRAND:
558 strandColour.setSelected(true);
562 case ColourSchemeProperty.TURN:
563 turnColour.setSelected(true);
567 case ColourSchemeProperty.BURIED:
568 buriedColour.setSelected(true);
572 case ColourSchemeProperty.NUCLEOTIDE:
573 nucleotideColour.setSelected(true);
577 case ColourSchemeProperty.TCOFFEE:
578 tcoffeeColour.setSelected(true);
581 case ColourSchemeProperty.PURINEPYRIMIDINE:
582 purinePyrimidineColour.setSelected(true);
586 case ColourSchemeProperty.RNAINTERACTION:
587 RNAInteractionColour.setSelected(true);
591 * case ColourSchemeProperty.COVARIATION:
592 * covariationColour.setSelected(true);
596 case ColourSchemeProperty.USER_DEFINED:
597 userDefinedColour.setSelected(true);
600 case ColourSchemeProperty.NONE:
602 noColourmenuItem.setSelected(true);
610 private void jbInit() throws Exception
612 fileMenu.setText(MessageManager.getString("action.file"));
613 saveAs.setText(MessageManager.getString("action.save_as") + "...");
614 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
615 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
616 .getMenuShortcutKeyMask()
617 | java.awt.event.KeyEvent.SHIFT_MASK, false));
618 saveAs.addActionListener(new ActionListener()
621 public void actionPerformed(ActionEvent e)
623 saveAs_actionPerformed(e);
626 closeMenuItem.setText(MessageManager.getString("action.close"));
627 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
628 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
629 .getMenuShortcutKeyMask(), false));
630 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
633 public void actionPerformed(ActionEvent e)
635 closeMenuItem_actionPerformed(false);
638 editMenu.setText(MessageManager.getString("action.edit"));
639 viewMenu.setText(MessageManager.getString("action.view"));
640 annotationsMenu.setText(MessageManager.getString("action.annotations"));
641 colourMenu.setText(MessageManager.getString("action.colour"));
642 calculateMenu.setText(MessageManager.getString("action.calculate"));
643 webService.setText(MessageManager.getString("action.web_service"));
644 selectAllSequenceMenuItem.setText(MessageManager
645 .getString("action.select_all"));
646 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
647 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
648 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
649 selectAllSequenceMenuItem
650 .addActionListener(new java.awt.event.ActionListener()
653 public void actionPerformed(ActionEvent e)
655 selectAllSequenceMenuItem_actionPerformed(e);
658 deselectAllSequenceMenuItem.setText(MessageManager
659 .getString("action.deselect_all"));
660 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
661 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
662 deselectAllSequenceMenuItem
663 .addActionListener(new java.awt.event.ActionListener()
666 public void actionPerformed(ActionEvent e)
668 deselectAllSequenceMenuItem_actionPerformed(e);
671 invertSequenceMenuItem.setText(MessageManager
672 .getString("action.invert_sequence_selection"));
673 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
674 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
675 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
676 invertSequenceMenuItem
677 .addActionListener(new java.awt.event.ActionListener()
680 public void actionPerformed(ActionEvent e)
682 invertSequenceMenuItem_actionPerformed(e);
685 grpsFromSelection.setText(MessageManager
686 .getString("action.make_groups_selection"));
687 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
690 public void actionPerformed(ActionEvent e)
692 makeGrpsFromSelection_actionPerformed(e);
695 expandAlignment.setText(MessageManager
696 .getString("action.view_flanking_regions"));
697 expandAlignment.setToolTipText(MessageManager
698 .getString("label.view_flanking_regions"));
699 expandAlignment.addActionListener(new java.awt.event.ActionListener()
702 public void actionPerformed(ActionEvent e)
707 remove2LeftMenuItem.setText(MessageManager
708 .getString("action.remove_left"));
709 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
710 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
711 .getMenuShortcutKeyMask(), false));
713 .addActionListener(new java.awt.event.ActionListener()
716 public void actionPerformed(ActionEvent e)
718 remove2LeftMenuItem_actionPerformed(e);
721 remove2RightMenuItem.setText(MessageManager
722 .getString("action.remove_right"));
723 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
724 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
725 .getMenuShortcutKeyMask(), false));
727 .addActionListener(new java.awt.event.ActionListener()
730 public void actionPerformed(ActionEvent e)
732 remove2RightMenuItem_actionPerformed(e);
735 removeGappedColumnMenuItem.setText(MessageManager
736 .getString("action.remove_empty_columns"));
737 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
738 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
739 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
740 removeGappedColumnMenuItem
741 .addActionListener(new java.awt.event.ActionListener()
744 public void actionPerformed(ActionEvent e)
746 removeGappedColumnMenuItem_actionPerformed(e);
749 removeAllGapsMenuItem.setText(MessageManager
750 .getString("action.remove_all_gaps"));
751 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
752 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
753 .getDefaultToolkit().getMenuShortcutKeyMask()
754 | java.awt.event.KeyEvent.SHIFT_MASK, false));
755 removeAllGapsMenuItem
756 .addActionListener(new java.awt.event.ActionListener()
759 public void actionPerformed(ActionEvent e)
761 removeAllGapsMenuItem_actionPerformed(e);
764 justifyLeftMenuItem.setText(MessageManager
765 .getString("action.left_justify_alignment"));
767 .addActionListener(new java.awt.event.ActionListener()
770 public void actionPerformed(ActionEvent e)
772 justifyLeftMenuItem_actionPerformed(e);
775 justifyRightMenuItem.setText(MessageManager
776 .getString("action.right_justify_alignment"));
778 .addActionListener(new java.awt.event.ActionListener()
781 public void actionPerformed(ActionEvent e)
783 justifyRightMenuItem_actionPerformed(e);
786 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
787 viewBoxesMenuItem.setState(true);
788 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
791 public void actionPerformed(ActionEvent e)
793 viewBoxesMenuItem_actionPerformed(e);
796 viewTextMenuItem.setText(MessageManager.getString("action.text"));
797 viewTextMenuItem.setState(true);
798 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
801 public void actionPerformed(ActionEvent e)
803 viewTextMenuItem_actionPerformed(e);
806 showNonconservedMenuItem.setText(MessageManager
807 .getString("label.show_non_conversed"));
808 showNonconservedMenuItem.setState(false);
809 showNonconservedMenuItem
810 .addActionListener(new java.awt.event.ActionListener()
813 public void actionPerformed(ActionEvent e)
815 showUnconservedMenuItem_actionPerformed(e);
818 sortPairwiseMenuItem.setText(MessageManager
819 .getString("action.by_pairwise_id"));
821 .addActionListener(new java.awt.event.ActionListener()
824 public void actionPerformed(ActionEvent e)
826 sortPairwiseMenuItem_actionPerformed(e);
829 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
830 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
833 public void actionPerformed(ActionEvent e)
835 sortIDMenuItem_actionPerformed(e);
839 .setText(MessageManager.getString("action.by_length"));
841 .addActionListener(new java.awt.event.ActionListener()
844 public void actionPerformed(ActionEvent e)
846 sortLengthMenuItem_actionPerformed(e);
849 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
850 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
853 public void actionPerformed(ActionEvent e)
855 sortGroupMenuItem_actionPerformed(e);
858 removeRedundancyMenuItem.setText(MessageManager
859 .getString("action.remove_redundancy").concat("..."));
860 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
861 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
862 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
863 removeRedundancyMenuItem
864 .addActionListener(new java.awt.event.ActionListener()
867 public void actionPerformed(ActionEvent e)
869 removeRedundancyMenuItem_actionPerformed(e);
872 pairwiseAlignmentMenuItem.setText(MessageManager
873 .getString("action.pairwise_alignment"));
874 pairwiseAlignmentMenuItem
875 .addActionListener(new java.awt.event.ActionListener()
878 public void actionPerformed(ActionEvent e)
880 pairwiseAlignmentMenuItem_actionPerformed(e);
883 PCAMenuItem.setText(MessageManager
884 .getString("label.principal_component_analysis"));
885 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
888 public void actionPerformed(ActionEvent e)
890 PCAMenuItem_actionPerformed(e);
893 averageDistanceTreeMenuItem.setText(MessageManager
894 .getString("label.average_distance_identity"));
895 averageDistanceTreeMenuItem
896 .addActionListener(new java.awt.event.ActionListener()
899 public void actionPerformed(ActionEvent e)
901 averageDistanceTreeMenuItem_actionPerformed(e);
904 neighbourTreeMenuItem.setText(MessageManager
905 .getString("label.neighbour_joining_identity"));
906 neighbourTreeMenuItem
907 .addActionListener(new java.awt.event.ActionListener()
910 public void actionPerformed(ActionEvent e)
912 neighbourTreeMenuItem_actionPerformed(e);
915 this.getContentPane().setLayout(borderLayout1);
916 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
917 statusBar.setBackground(Color.white);
918 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
919 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
920 statusBar.setText(MessageManager.getString("label.status_bar"));
921 outputTextboxMenu.setText(MessageManager
922 .getString("label.out_to_textbox"));
923 clustalColour.setText(MessageManager.getString("label.clustalx"));
925 clustalColour.addActionListener(new java.awt.event.ActionListener()
928 public void actionPerformed(ActionEvent e)
930 clustalColour_actionPerformed(e);
933 zappoColour.setText(MessageManager.getString("label.zappo"));
934 zappoColour.addActionListener(new java.awt.event.ActionListener()
937 public void actionPerformed(ActionEvent e)
939 zappoColour_actionPerformed(e);
942 taylorColour.setText(MessageManager.getString("label.taylor"));
943 taylorColour.addActionListener(new java.awt.event.ActionListener()
946 public void actionPerformed(ActionEvent e)
948 taylorColour_actionPerformed(e);
951 hydrophobicityColour.setText(MessageManager
952 .getString("label.hydrophobicity"));
954 .addActionListener(new java.awt.event.ActionListener()
957 public void actionPerformed(ActionEvent e)
959 hydrophobicityColour_actionPerformed(e);
962 helixColour.setText(MessageManager.getString("label.helix_propensity"));
963 helixColour.addActionListener(new java.awt.event.ActionListener()
966 public void actionPerformed(ActionEvent e)
968 helixColour_actionPerformed(e);
971 strandColour.setText(MessageManager
972 .getString("label.strand_propensity"));
973 strandColour.addActionListener(new java.awt.event.ActionListener()
976 public void actionPerformed(ActionEvent e)
978 strandColour_actionPerformed(e);
981 turnColour.setText(MessageManager.getString("label.turn_propensity"));
982 turnColour.addActionListener(new java.awt.event.ActionListener()
985 public void actionPerformed(ActionEvent e)
987 turnColour_actionPerformed(e);
990 buriedColour.setText(MessageManager.getString("label.buried_index"));
991 buriedColour.addActionListener(new java.awt.event.ActionListener()
994 public void actionPerformed(ActionEvent e)
996 buriedColour_actionPerformed(e);
999 userDefinedColour.setText(MessageManager
1000 .getString("action.user_defined"));
1001 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1004 public void actionPerformed(ActionEvent e)
1006 userDefinedColour_actionPerformed(e);
1010 .setText(MessageManager.getString("label.percentage_identity"));
1011 PIDColour.addActionListener(new java.awt.event.ActionListener()
1014 public void actionPerformed(ActionEvent e)
1016 PIDColour_actionPerformed(e);
1020 .setText(MessageManager.getString("label.blosum62_score"));
1021 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1024 public void actionPerformed(ActionEvent e)
1026 BLOSUM62Colour_actionPerformed(e);
1029 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1030 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1033 public void actionPerformed(ActionEvent e)
1035 nucleotideColour_actionPerformed(e);
1039 purinePyrimidineColour.setText(MessageManager
1040 .getString("label.purine_pyrimidine"));
1041 purinePyrimidineColour
1042 .addActionListener(new java.awt.event.ActionListener()
1045 public void actionPerformed(ActionEvent e)
1047 purinePyrimidineColour_actionPerformed(e);
1051 RNAInteractionColour.setText("RNA Interaction type");
1052 RNAInteractionColour
1053 .addActionListener(new java.awt.event.ActionListener()
1056 public void actionPerformed(ActionEvent e)
1058 RNAInteractionColour_actionPerformed(e);
1062 * covariationColour.setText("Covariation");
1063 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1064 * public void actionPerformed(ActionEvent e) {
1065 * covariationColour_actionPerformed(e); } });
1068 avDistanceTreeBlosumMenuItem.setText(MessageManager
1069 .getString("label.average_distance_bloslum62"));
1070 avDistanceTreeBlosumMenuItem
1071 .addActionListener(new java.awt.event.ActionListener()
1074 public void actionPerformed(ActionEvent e)
1076 avTreeBlosumMenuItem_actionPerformed(e);
1079 njTreeBlosumMenuItem.setText(MessageManager
1080 .getString("label.neighbour_blosum62"));
1081 njTreeBlosumMenuItem
1082 .addActionListener(new java.awt.event.ActionListener()
1085 public void actionPerformed(ActionEvent e)
1087 njTreeBlosumMenuItem_actionPerformed(e);
1090 annotationPanelMenuItem.setActionCommand("");
1091 annotationPanelMenuItem.setText(MessageManager
1092 .getString("label.show_annotations"));
1093 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1095 annotationPanelMenuItem.addActionListener(new ActionListener()
1098 public void actionPerformed(ActionEvent e)
1100 annotationPanelMenuItem_actionPerformed(e);
1103 showAllAlAnnotations.setText(MessageManager
1104 .getString("label.show_all_al_annotations"));
1105 final boolean isAnnotationPanelShown = annotationPanelMenuItem
1107 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1108 showAllAlAnnotations.addActionListener(new ActionListener()
1111 public void actionPerformed(ActionEvent e)
1113 showAllAnnotations_actionPerformed(false, true);
1116 hideAllAlAnnotations.setText(MessageManager
1117 .getString("label.hide_all_al_annotations"));
1118 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1119 hideAllAlAnnotations.addActionListener(new ActionListener()
1122 public void actionPerformed(ActionEvent e)
1124 hideAllAnnotations_actionPerformed(false, true);
1127 showAllSeqAnnotations.setText(MessageManager
1128 .getString("label.show_all_seq_annotations"));
1129 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1130 showAllSeqAnnotations.addActionListener(new ActionListener()
1133 public void actionPerformed(ActionEvent e)
1135 showAllAnnotations_actionPerformed(true, false);
1138 hideAllSeqAnnotations.setText(MessageManager
1139 .getString("label.hide_all_seq_annotations"));
1140 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1141 hideAllSeqAnnotations.addActionListener(new ActionListener()
1144 public void actionPerformed(ActionEvent e)
1146 hideAllAnnotations_actionPerformed(true, false);
1149 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
1150 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
1151 SequenceAnnotationOrder.NONE.name()));
1152 sortAnnBySequence.setText(MessageManager
1153 .getString("label.sort_annotations_by_sequence"));
1155 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
1156 sortAnnBySequence.addActionListener(new ActionListener()
1159 public void actionPerformed(ActionEvent e)
1161 boolean newState = sortAnnBySequence.getState();
1162 sortAnnByLabel.setSelected(false);
1163 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1164 : SequenceAnnotationOrder.NONE);
1165 sortAnnotations_actionPerformed();
1168 sortAnnByLabel.setText(MessageManager
1169 .getString("label.sort_annotations_by_label"));
1171 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1172 sortAnnByLabel.addActionListener(new ActionListener()
1175 public void actionPerformed(ActionEvent e)
1177 boolean newState = sortAnnByLabel.getState();
1178 sortAnnBySequence.setSelected(false);
1179 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1180 : SequenceAnnotationOrder.NONE);
1181 sortAnnotations_actionPerformed();
1184 colourTextMenuItem.setText(MessageManager
1185 .getString("label.colour_text"));
1187 .addActionListener(new java.awt.event.ActionListener()
1190 public void actionPerformed(ActionEvent e)
1192 colourTextMenuItem_actionPerformed(e);
1195 htmlMenuItem.setText(MessageManager.getString("label.html"));
1196 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1199 public void actionPerformed(ActionEvent e)
1201 htmlMenuItem_actionPerformed(e);
1205 // TODO uncomment when supported by MassageManager
1206 // createBioJS.setText(MessageManager.getString("label.biojs_html_export"));
1207 createBioJS.setText("BioJS");
1208 createBioJS.addActionListener(new java.awt.event.ActionListener()
1211 public void actionPerformed(ActionEvent e)
1213 bioJSMenuItem_actionPerformed(e);
1217 overviewMenuItem.setText(MessageManager
1218 .getString("label.overview_window"));
1219 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1222 public void actionPerformed(ActionEvent e)
1224 overviewMenuItem_actionPerformed(e);
1227 undoMenuItem.setEnabled(false);
1228 undoMenuItem.setText(MessageManager.getString("action.undo"));
1229 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1230 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1231 .getMenuShortcutKeyMask(), false));
1232 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1235 public void actionPerformed(ActionEvent e)
1237 undoMenuItem_actionPerformed(e);
1240 redoMenuItem.setEnabled(false);
1241 redoMenuItem.setText(MessageManager.getString("action.redo"));
1242 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1243 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1244 .getMenuShortcutKeyMask(), false));
1245 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1248 public void actionPerformed(ActionEvent e)
1250 redoMenuItem_actionPerformed(e);
1253 conservationMenuItem.setText(MessageManager
1254 .getString("action.by_conservation"));
1255 conservationMenuItem
1256 .addActionListener(new java.awt.event.ActionListener()
1259 public void actionPerformed(ActionEvent e)
1261 conservationMenuItem_actionPerformed(e);
1264 noColourmenuItem.setText(MessageManager.getString("label.none"));
1265 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1268 public void actionPerformed(ActionEvent e)
1270 noColourmenuItem_actionPerformed(e);
1273 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1274 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1277 public void actionPerformed(ActionEvent e)
1279 wrapMenuItem_actionPerformed(e);
1282 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1283 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1284 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1285 .getMenuShortcutKeyMask(), false));
1286 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1289 public void actionPerformed(ActionEvent e)
1291 printMenuItem_actionPerformed(e);
1295 .setText(MessageManager.getString("action.show_gaps"));
1296 renderGapsMenuItem.setState(true);
1298 .addActionListener(new java.awt.event.ActionListener()
1301 public void actionPerformed(ActionEvent e)
1303 renderGapsMenuItem_actionPerformed(e);
1306 findMenuItem.setText(MessageManager.getString("action.find"));
1307 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1308 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1309 .getMenuShortcutKeyMask(), false));
1310 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1311 MessageManager.getString("label.find_tip")));
1312 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1315 public void actionPerformed(ActionEvent e)
1317 findMenuItem_actionPerformed(e);
1320 abovePIDThreshold.setText(MessageManager
1321 .getString("label.above_identity_threshold"));
1322 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1325 public void actionPerformed(ActionEvent e)
1327 abovePIDThreshold_actionPerformed(e);
1330 showSeqFeatures.setText(MessageManager
1331 .getString("label.show_sequence_features"));
1332 showSeqFeatures.addActionListener(new ActionListener()
1335 public void actionPerformed(ActionEvent actionEvent)
1337 showSeqFeatures_actionPerformed(actionEvent);
1341 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1342 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1343 * void actionPerformed(ActionEvent actionEvent) {
1344 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1346 showDbRefsMenuitem.setText(MessageManager
1347 .getString("label.show_database_refs"));
1348 showDbRefsMenuitem.addActionListener(new ActionListener()
1352 public void actionPerformed(ActionEvent e)
1354 showDbRefs_actionPerformed(e);
1358 showNpFeatsMenuitem.setText(MessageManager
1359 .getString("label.show_non_positional_features"));
1360 showNpFeatsMenuitem.addActionListener(new ActionListener()
1364 public void actionPerformed(ActionEvent e)
1366 showNpFeats_actionPerformed(e);
1370 showGroupConservation.setText(MessageManager
1371 .getString("label.group_conservation"));
1372 showGroupConservation.addActionListener(new ActionListener()
1376 public void actionPerformed(ActionEvent e)
1378 showGroupConservation_actionPerformed(e);
1383 showGroupConsensus.setText(MessageManager
1384 .getString("label.group_consensus"));
1385 showGroupConsensus.addActionListener(new ActionListener()
1389 public void actionPerformed(ActionEvent e)
1391 showGroupConsensus_actionPerformed(e);
1395 showConsensusHistogram.setText(MessageManager
1396 .getString("label.show_consensus_histogram"));
1397 showConsensusHistogram.addActionListener(new ActionListener()
1401 public void actionPerformed(ActionEvent e)
1403 showConsensusHistogram_actionPerformed(e);
1407 showSequenceLogo.setText(MessageManager
1408 .getString("label.show_consensus_logo"));
1409 showSequenceLogo.addActionListener(new ActionListener()
1413 public void actionPerformed(ActionEvent e)
1415 showSequenceLogo_actionPerformed(e);
1419 normaliseSequenceLogo.setText(MessageManager
1420 .getString("label.norm_consensus_logo"));
1421 normaliseSequenceLogo.addActionListener(new ActionListener()
1425 public void actionPerformed(ActionEvent e)
1427 normaliseSequenceLogo_actionPerformed(e);
1431 applyAutoAnnotationSettings.setText(MessageManager
1432 .getString("label.apply_all_groups"));
1433 applyAutoAnnotationSettings.setState(false);
1434 applyAutoAnnotationSettings.setVisible(true);
1435 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1438 public void actionPerformed(ActionEvent e)
1440 applyAutoAnnotationSettings_actionPerformed(e);
1444 ButtonGroup buttonGroup = new ButtonGroup();
1445 buttonGroup.add(showAutoFirst);
1446 buttonGroup.add(showAutoLast);
1447 showAutoFirst.setText(MessageManager.getString("label.show_first"));
1448 showAutoFirst.setSelected(Cache.getDefault(
1449 Preferences.SHOW_AUTOCALC_ABOVE,
1451 showAutoFirst.addActionListener(new ActionListener()
1454 public void actionPerformed(ActionEvent e)
1456 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1457 sortAnnotations_actionPerformed();
1460 showAutoLast.setText(MessageManager.getString("label.show_last"));
1461 showAutoLast.setSelected(!showAutoFirst.isSelected());
1462 showAutoLast.addActionListener(new ActionListener()
1465 public void actionPerformed(ActionEvent e)
1467 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1468 sortAnnotations_actionPerformed();
1472 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1473 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1476 public void actionPerformed(ActionEvent e)
1478 nucleotideColour_actionPerformed(e);
1482 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1483 tcoffeeColour.setEnabled(false);
1484 tcoffeeColour.addActionListener(new ActionListener()
1488 public void actionPerformed(ActionEvent e)
1490 tcoffeeColorScheme_actionPerformed(e);
1495 .setText(MessageManager.getString("action.undefine_groups"));
1496 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1497 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1498 .getMenuShortcutKeyMask(), false));
1499 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1502 public void actionPerformed(ActionEvent e)
1504 deleteGroups_actionPerformed(e);
1507 createGroup.setText(MessageManager.getString("action.create_groups"));
1508 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1509 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1510 .getMenuShortcutKeyMask(), false));
1511 createGroup.addActionListener(new java.awt.event.ActionListener()
1514 public void actionPerformed(ActionEvent e)
1516 createGroup_actionPerformed(e);
1519 unGroup.setText(MessageManager.getString("action.remove_group"));
1520 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1521 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1522 .getMenuShortcutKeyMask()
1523 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1524 unGroup.addActionListener(new java.awt.event.ActionListener()
1527 public void actionPerformed(ActionEvent e)
1529 unGroup_actionPerformed(e);
1532 copy.setText(MessageManager.getString("action.copy"));
1533 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1534 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1535 .getMenuShortcutKeyMask(), false));
1537 copy.addActionListener(new java.awt.event.ActionListener()
1540 public void actionPerformed(ActionEvent e)
1542 copy_actionPerformed(e);
1545 cut.setText(MessageManager.getString("action.cut"));
1546 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1547 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1548 .getMenuShortcutKeyMask(), false));
1549 cut.addActionListener(new java.awt.event.ActionListener()
1552 public void actionPerformed(ActionEvent e)
1554 cut_actionPerformed(e);
1557 delete.setText(MessageManager.getString("action.delete"));
1558 delete.addActionListener(new java.awt.event.ActionListener()
1561 public void actionPerformed(ActionEvent e)
1563 delete_actionPerformed(e);
1566 pasteMenu.setText(MessageManager.getString("action.paste"));
1567 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1568 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1569 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1570 .getMenuShortcutKeyMask()
1571 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1572 pasteNew.addActionListener(new java.awt.event.ActionListener()
1575 public void actionPerformed(ActionEvent e)
1577 pasteNew_actionPerformed(e);
1580 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1581 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1582 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1583 .getMenuShortcutKeyMask(), false));
1584 pasteThis.addActionListener(new java.awt.event.ActionListener()
1587 public void actionPerformed(ActionEvent e)
1589 pasteThis_actionPerformed(e);
1592 applyToAllGroups.setText(MessageManager
1593 .getString("label.apply_colour_to_all_groups"));
1594 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1597 public void actionPerformed(ActionEvent e)
1599 applyToAllGroups_actionPerformed(e);
1602 createPNG.addActionListener(new java.awt.event.ActionListener()
1605 public void actionPerformed(ActionEvent e)
1610 createPNG.setActionCommand(MessageManager
1611 .getString("label.save_png_image"));
1612 createPNG.setText("PNG");
1614 font.setText(MessageManager.getString("action.font"));
1615 font.addActionListener(new java.awt.event.ActionListener()
1618 public void actionPerformed(ActionEvent e)
1620 font_actionPerformed(e);
1623 seqLimits.setText(MessageManager
1624 .getString("label.show_sequence_limits"));
1625 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1626 seqLimits.addActionListener(new java.awt.event.ActionListener()
1629 public void actionPerformed(ActionEvent e)
1631 seqLimit_actionPerformed(e);
1634 epsFile.setText("EPS");
1635 epsFile.addActionListener(new java.awt.event.ActionListener()
1638 public void actionPerformed(ActionEvent e)
1644 createSVG.setText("SVG");
1645 createSVG.addActionListener(new java.awt.event.ActionListener()
1648 public void actionPerformed(ActionEvent e)
1654 LoadtreeMenuItem.setActionCommand(MessageManager
1655 .getString("label.load_tree_for_sequence_set"));
1656 LoadtreeMenuItem.setText(MessageManager
1657 .getString("label.load_associated_tree"));
1658 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1661 public void actionPerformed(ActionEvent e)
1663 LoadtreeMenuItem_actionPerformed(e);
1667 scaleAbove.setVisible(false);
1668 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1669 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1672 public void actionPerformed(ActionEvent e)
1674 scaleAbove_actionPerformed(e);
1677 scaleLeft.setVisible(false);
1678 scaleLeft.setSelected(true);
1679 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1680 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1683 public void actionPerformed(ActionEvent e)
1685 scaleLeft_actionPerformed(e);
1688 scaleRight.setVisible(false);
1689 scaleRight.setSelected(true);
1690 scaleRight.setText(MessageManager.getString("action.scale_right"));
1691 scaleRight.addActionListener(new java.awt.event.ActionListener()
1694 public void actionPerformed(ActionEvent e)
1696 scaleRight_actionPerformed(e);
1699 centreColumnLabelsMenuItem.setVisible(true);
1700 centreColumnLabelsMenuItem.setState(false);
1701 centreColumnLabelsMenuItem.setText(MessageManager
1702 .getString("label.centre_column_labels"));
1703 centreColumnLabelsMenuItem
1704 .addActionListener(new java.awt.event.ActionListener()
1707 public void actionPerformed(ActionEvent e)
1709 centreColumnLabels_actionPerformed(e);
1712 followHighlightMenuItem.setVisible(true);
1713 followHighlightMenuItem.setState(true);
1714 followHighlightMenuItem.setText(MessageManager
1715 .getString("label.automatic_scrolling"));
1716 followHighlightMenuItem.addActionListener(new ActionListener()
1720 public void actionPerformed(ActionEvent e)
1722 followHighlight_actionPerformed();
1727 modifyPID.setText(MessageManager
1728 .getString("label.modify_identity_thereshold"));
1729 modifyPID.addActionListener(new java.awt.event.ActionListener()
1732 public void actionPerformed(ActionEvent e)
1734 modifyPID_actionPerformed(e);
1737 modifyConservation.setText(MessageManager
1738 .getString("label.modify_conservation_thereshold"));
1740 .addActionListener(new java.awt.event.ActionListener()
1743 public void actionPerformed(ActionEvent e)
1745 modifyConservation_actionPerformed(e);
1749 .setText(MessageManager.getString("action.by_tree_order"));
1750 sort.setText(MessageManager.getString("action.sort"));
1751 sort.addMenuListener(new MenuListener()
1754 public void menuSelected(MenuEvent e)
1760 public void menuDeselected(MenuEvent e)
1765 public void menuCanceled(MenuEvent e)
1769 sortByAnnotScore.setText(MessageManager
1770 .getString("label.sort_by_score"));
1771 sort.add(sortByAnnotScore);
1772 sort.addMenuListener(new javax.swing.event.MenuListener()
1776 public void menuCanceled(MenuEvent e)
1781 public void menuDeselected(MenuEvent e)
1786 public void menuSelected(MenuEvent e)
1788 buildSortByAnnotationScoresMenu();
1791 sortByAnnotScore.setVisible(false);
1794 .setText(MessageManager.getString("action.calculate_tree"));
1796 jMenu2.setText(MessageManager.getString("label.export_image"));
1797 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1798 padGapsMenuitem.setState(jalview.bin.Cache
1799 .getDefault("PAD_GAPS", false));
1800 padGapsMenuitem.addActionListener(new ActionListener()
1803 public void actionPerformed(ActionEvent e)
1805 padGapsMenuitem_actionPerformed(e);
1808 vamsasStore.setVisible(false);
1809 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1810 vamsasStore.addActionListener(new ActionListener()
1813 public void actionPerformed(ActionEvent e)
1815 vamsasStore_actionPerformed(e);
1818 showTranslation.setText(MessageManager
1819 .getString("label.translate_cDNA"));
1820 showTranslation.addActionListener(new ActionListener()
1823 public void actionPerformed(ActionEvent e)
1825 showTranslation_actionPerformed(e);
1828 extractScores.setText(MessageManager.getString("label.extract_scores")
1830 extractScores.addActionListener(new ActionListener()
1833 public void actionPerformed(ActionEvent e)
1835 extractScores_actionPerformed(e);
1838 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1840 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1842 * showProducts.addActionListener(new ActionListener() {
1844 * public void actionPerformed(ActionEvent e) {
1845 * showProducts_actionPerformed(e); } });
1847 openFeatureSettings.setText(MessageManager
1848 .getString("label.feature_settings"));
1849 openFeatureSettings.addActionListener(new ActionListener()
1852 public void actionPerformed(ActionEvent e)
1854 featureSettings_actionPerformed(e);
1858 .setText(MessageManager.getString("label.fetch_sequences"));
1859 fetchSequence.addActionListener(new ActionListener()
1862 public void actionPerformed(ActionEvent e)
1864 fetchSequence_actionPerformed(e);
1868 annotationColour.setText(MessageManager
1869 .getString("action.by_annotation"));
1870 annotationColour.addActionListener(new ActionListener()
1873 public void actionPerformed(ActionEvent e)
1875 annotationColour_actionPerformed(e);
1879 annotationColumn.setText("Select by annotation...");
1880 annotationColumn.addActionListener(new ActionListener()
1883 public void actionPerformed(ActionEvent e)
1885 annotationColumn_actionPerformed(e);
1889 rnahelicesColour.setText(MessageManager
1890 .getString("action.by_rna_helixes"));
1891 rnahelicesColour.addActionListener(new ActionListener()
1894 public void actionPerformed(ActionEvent e)
1896 rnahelicesColour_actionPerformed(e);
1900 associatedData.setText(MessageManager
1901 .getString("label.load_features_annotations"));
1902 associatedData.addActionListener(new ActionListener()
1905 public void actionPerformed(ActionEvent e)
1907 associatedData_actionPerformed(e);
1910 autoCalculate.setText(MessageManager
1911 .getString("label.autocalculate_consensus"));
1912 autoCalculate.setState(jalview.bin.Cache.getDefault(
1913 "AUTO_CALC_CONSENSUS", true));
1914 autoCalculate.addActionListener(new ActionListener()
1917 public void actionPerformed(ActionEvent e)
1919 autoCalculate_actionPerformed(e);
1922 sortByTree.setText(MessageManager
1923 .getString("label.sort_alignment_new_tree"));
1925 .setToolTipText("<html>"
1927 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1929 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1930 sortByTree.addActionListener(new ActionListener()
1933 public void actionPerformed(ActionEvent e)
1935 sortByTreeOption_actionPerformed(e);
1939 listenToViewSelections.setText(MessageManager
1940 .getString("label.listen_for_selections"));
1941 listenToViewSelections
1942 .setToolTipText("<html>"
1944 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1945 listenToViewSelections.setState(false);
1946 listenToViewSelections.addActionListener(new ActionListener()
1949 public void actionPerformed(ActionEvent e)
1951 listenToViewSelections_actionPerformed(e);
1956 .setText(MessageManager.getString("label.add_sequences"));
1957 addFromFile.setText(MessageManager.getString("label.from_file"));
1958 addFromFile.addActionListener(new ActionListener()
1961 public void actionPerformed(ActionEvent e)
1963 addFromFile_actionPerformed(e);
1966 addFromText.setText(MessageManager.getString("label.from_textbox"));
1967 addFromText.addActionListener(new ActionListener()
1970 public void actionPerformed(ActionEvent e)
1972 addFromText_actionPerformed(e);
1975 addFromURL.setText(MessageManager.getString("label.from_url"));
1976 addFromURL.addActionListener(new ActionListener()
1979 public void actionPerformed(ActionEvent e)
1981 addFromURL_actionPerformed(e);
1984 exportFeatures.setText(MessageManager
1985 .getString("label.export_features"));
1986 exportFeatures.addActionListener(new ActionListener()
1989 public void actionPerformed(ActionEvent e)
1991 exportFeatures_actionPerformed(e);
1994 exportAnnotations.setText(MessageManager
1995 .getString("label.export_annotations"));
1996 exportAnnotations.addActionListener(new ActionListener()
1999 public void actionPerformed(ActionEvent e)
2001 exportAnnotations_actionPerformed(e);
2004 statusPanel.setLayout(gridLayout1);
2005 jMenu3.setText(MessageManager.getString("action.show"));
2006 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
2007 showAllSeqs.setToolTipText(MessageManager
2008 .getString("label.toggle_sequence_visibility"));
2009 showAllSeqs.addActionListener(new ActionListener()
2012 public void actionPerformed(ActionEvent e)
2014 showAllSeqs_actionPerformed(e);
2017 showAllColumns.setText(MessageManager.getString("label.all_columns"));
2018 showAllColumns.setToolTipText(MessageManager
2019 .getString("label.toggle_columns_visibility"));
2020 showAllColumns.addActionListener(new ActionListener()
2023 public void actionPerformed(ActionEvent e)
2025 showAllColumns_actionPerformed(e);
2028 hideMenu.setText(MessageManager.getString("action.hide"));
2029 hideSelSequences.setText(MessageManager
2030 .getString("label.selected_sequences"));
2031 hideSelSequences.setToolTipText(MessageManager
2032 .getString("label.toggle_sequence_visibility"));
2033 hideSelSequences.addActionListener(new ActionListener()
2036 public void actionPerformed(ActionEvent e)
2038 hideSelSequences_actionPerformed(e);
2041 hideSelColumns.setText(MessageManager
2042 .getString("label.selected_columns"));
2043 hideSelColumns.setToolTipText(MessageManager
2044 .getString("label.toggle_columns_visibility"));
2045 hideSelColumns.addActionListener(new ActionListener()
2048 public void actionPerformed(ActionEvent e)
2050 hideSelColumns_actionPerformed(e);
2053 hideAllSelection.setText(MessageManager
2054 .getString("label.selected_region"));
2055 hideAllSelection.addActionListener(new ActionListener()
2058 public void actionPerformed(ActionEvent e)
2060 hideAllSelection_actionPerformed(e);
2063 // TODO: should be hidden if no selection exists.
2064 hideAllButSelection.setText(MessageManager
2065 .getString("label.all_but_selected_region"));
2066 hideAllButSelection.addActionListener(new ActionListener()
2069 public void actionPerformed(ActionEvent e)
2071 hideAllButSelection_actionPerformed(e);
2074 showAllhidden.setText(MessageManager
2075 .getString("label.all_sequences_columns"));
2076 showAllhidden.setToolTipText(MessageManager
2077 .getString("label.toggles_visibility_hidden_selected_regions"));
2078 showAllhidden.addActionListener(new ActionListener()
2081 public void actionPerformed(ActionEvent e)
2083 showAllhidden_actionPerformed(e);
2086 hiddenMarkers.setText(MessageManager
2087 .getString("action.show_hidden_markers"));
2088 hiddenMarkers.addActionListener(new ActionListener()
2091 public void actionPerformed(ActionEvent e)
2093 hiddenMarkers_actionPerformed(e);
2096 invertColSel.setText(MessageManager
2097 .getString("action.invert_column_selection"));
2098 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2099 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
2100 .getMenuShortcutKeyMask()
2101 | java.awt.event.KeyEvent.ALT_MASK, false));
2102 invertColSel.addActionListener(new ActionListener()
2105 public void actionPerformed(ActionEvent e)
2107 invertColSel_actionPerformed(e);
2110 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2113 public void stateChanged(ChangeEvent evt)
2115 JTabbedPane pane = (JTabbedPane) evt.getSource();
2116 int sel = pane.getSelectedIndex();
2117 tabSelectionChanged(sel);
2120 tabbedPane.addMouseListener(new MouseAdapter()
2123 public void mousePressed(MouseEvent e)
2125 tabbedPane_mousePressed(e);
2128 tabbedPane.addFocusListener(new FocusAdapter()
2131 public void focusGained(FocusEvent e)
2133 tabbedPane_focusGained(e);
2136 save.setText(MessageManager.getString("action.save"));
2137 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2138 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2139 .getMenuShortcutKeyMask(), false));
2140 save.addActionListener(new ActionListener()
2143 public void actionPerformed(ActionEvent e)
2145 save_actionPerformed(e);
2148 reload.setEnabled(false);
2149 reload.setText(MessageManager.getString("action.reload"));
2150 reload.addActionListener(new ActionListener()
2153 public void actionPerformed(ActionEvent e)
2155 reload_actionPerformed(e);
2158 newView.setText(MessageManager.getString("action.new_view"));
2159 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2160 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2161 .getMenuShortcutKeyMask(), false));
2162 newView.addActionListener(new ActionListener()
2165 public void actionPerformed(ActionEvent e)
2167 newView_actionPerformed(e);
2170 tabbedPane.setToolTipText("<html><i>"
2171 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2173 textColour.setText(MessageManager.getString("label.colour_text")
2175 textColour.addActionListener(new ActionListener()
2178 public void actionPerformed(ActionEvent e)
2180 textColour_actionPerformed(e);
2183 formatMenu.setText(MessageManager.getString("action.format"));
2184 selectMenu.setText(MessageManager.getString("action.select"));
2185 idRightAlign.setText(MessageManager
2186 .getString("label.right_align_sequence_id"));
2187 idRightAlign.addActionListener(new ActionListener()
2190 public void actionPerformed(ActionEvent e)
2192 idRightAlign_actionPerformed(e);
2195 gatherViews.setEnabled(false);
2196 gatherViews.setText(MessageManager.getString("action.gather_views"));
2197 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2198 java.awt.event.KeyEvent.VK_G, 0, false));
2199 gatherViews.addActionListener(new ActionListener()
2202 public void actionPerformed(ActionEvent e)
2204 gatherViews_actionPerformed(e);
2207 expandViews.setEnabled(false);
2208 expandViews.setText(MessageManager.getString("action.expand_views"));
2209 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2210 java.awt.event.KeyEvent.VK_X, 0, false));
2211 expandViews.addActionListener(new ActionListener()
2214 public void actionPerformed(ActionEvent e)
2216 expandViews_actionPerformed(e);
2220 .setText(MessageManager.getString("action.page_setup") + "...");
2221 pageSetup.addActionListener(new ActionListener()
2224 public void actionPerformed(ActionEvent e)
2226 pageSetup_actionPerformed(e);
2229 alignmentProperties.setText(MessageManager
2230 .getString("label.alignment_props") + "...");
2231 alignmentProperties.addActionListener(new ActionListener()
2234 public void actionPerformed(ActionEvent actionEvent)
2236 alignmentProperties();
2239 tooltipSettingsMenu.setText(MessageManager
2240 .getString("label.sequence_id_tooltip"));
2241 autoAnnMenu.setText(MessageManager
2242 .getString("label.autocalculated_annotation"));
2243 alignFrameMenuBar.add(fileMenu);
2244 alignFrameMenuBar.add(editMenu);
2245 alignFrameMenuBar.add(selectMenu);
2246 alignFrameMenuBar.add(viewMenu);
2247 alignFrameMenuBar.add(annotationsMenu);
2248 alignFrameMenuBar.add(formatMenu);
2249 alignFrameMenuBar.add(colourMenu);
2250 alignFrameMenuBar.add(calculateMenu);
2251 alignFrameMenuBar.add(webService);
2252 fileMenu.add(fetchSequence);
2253 fileMenu.add(addSequenceMenu);
2254 fileMenu.add(reload);
2255 fileMenu.addSeparator();
2256 fileMenu.add(vamsasStore);
2258 fileMenu.add(saveAs);
2259 fileMenu.add(outputTextboxMenu);
2260 fileMenu.add(pageSetup);
2261 fileMenu.add(printMenuItem);
2262 fileMenu.addSeparator();
2263 fileMenu.add(jMenu2);
2264 fileMenu.add(exportFeatures);
2265 fileMenu.add(exportAnnotations);
2266 fileMenu.add(LoadtreeMenuItem);
2267 fileMenu.add(associatedData);
2268 fileMenu.addSeparator();
2269 fileMenu.add(closeMenuItem);
2270 editMenu.add(undoMenuItem);
2271 editMenu.add(redoMenuItem);
2274 editMenu.add(pasteMenu);
2275 editMenu.add(delete);
2276 editMenu.addSeparator();
2277 editMenu.add(remove2LeftMenuItem);
2278 editMenu.add(remove2RightMenuItem);
2279 editMenu.add(removeGappedColumnMenuItem);
2280 editMenu.add(removeAllGapsMenuItem);
2281 editMenu.add(removeRedundancyMenuItem);
2282 editMenu.addSeparator();
2283 // dont add these yet in the CVS build - they cannot be undone!
2284 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2285 // editMenu.add(justifyLeftMenuItem);
2286 // editMenu.add(justifyRightMenuItem);
2287 // editMenu.addSeparator();
2288 editMenu.add(padGapsMenuitem);
2289 viewMenu.add(newView);
2290 viewMenu.add(expandViews);
2291 viewMenu.add(gatherViews);
2292 viewMenu.addSeparator();
2293 viewMenu.add(jMenu3);
2294 viewMenu.add(hideMenu);
2295 viewMenu.addSeparator();
2296 viewMenu.add(followHighlightMenuItem);
2297 annotationsMenu.add(annotationPanelMenuItem);
2298 annotationsMenu.addSeparator();
2299 annotationsMenu.add(showAllAlAnnotations);
2300 annotationsMenu.add(hideAllAlAnnotations);
2301 annotationsMenu.addSeparator();
2302 annotationsMenu.add(showAllSeqAnnotations);
2303 annotationsMenu.add(hideAllSeqAnnotations);
2304 annotationsMenu.add(sortAnnBySequence);
2305 annotationsMenu.add(sortAnnByLabel);
2306 annotationsMenu.addSeparator();
2307 autoAnnMenu.add(showAutoFirst);
2308 autoAnnMenu.add(showAutoLast);
2309 autoAnnMenu.addSeparator();
2310 autoAnnMenu.add(applyAutoAnnotationSettings);
2311 autoAnnMenu.add(showConsensusHistogram);
2312 autoAnnMenu.add(showSequenceLogo);
2313 autoAnnMenu.add(normaliseSequenceLogo);
2314 autoAnnMenu.addSeparator();
2315 autoAnnMenu.add(showGroupConservation);
2316 autoAnnMenu.add(showGroupConsensus);
2317 annotationsMenu.add(autoAnnMenu);
2318 viewMenu.addSeparator();
2319 viewMenu.add(showSeqFeatures);
2320 // viewMenu.add(showSeqFeaturesHeight);
2322 viewMenu.add(openFeatureSettings);
2323 tooltipSettingsMenu.add(showDbRefsMenuitem);
2324 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2325 viewMenu.add(tooltipSettingsMenu);
2326 viewMenu.addSeparator();
2327 viewMenu.add(alignmentProperties);
2328 viewMenu.addSeparator();
2329 viewMenu.add(overviewMenuItem);
2330 colourMenu.add(applyToAllGroups);
2331 colourMenu.add(textColour);
2332 colourMenu.addSeparator();
2333 colourMenu.add(noColourmenuItem);
2334 colourMenu.add(clustalColour);
2335 colourMenu.add(BLOSUM62Colour);
2336 colourMenu.add(PIDColour);
2337 colourMenu.add(zappoColour);
2338 colourMenu.add(taylorColour);
2339 colourMenu.add(hydrophobicityColour);
2340 colourMenu.add(helixColour);
2341 colourMenu.add(strandColour);
2342 colourMenu.add(turnColour);
2343 colourMenu.add(buriedColour);
2344 colourMenu.add(nucleotideColour);
2345 colourMenu.add(purinePyrimidineColour);
2346 colourMenu.add(RNAInteractionColour);
2347 // colourMenu.add(covariationColour);
2348 colourMenu.add(tcoffeeColour);
2349 colourMenu.add(userDefinedColour);
2350 colourMenu.addSeparator();
2351 colourMenu.add(conservationMenuItem);
2352 colourMenu.add(modifyConservation);
2353 colourMenu.add(abovePIDThreshold);
2354 colourMenu.add(modifyPID);
2355 colourMenu.add(annotationColour);
2356 colourMenu.add(rnahelicesColour);
2357 calculateMenu.add(sort);
2358 calculateMenu.add(calculateTree);
2359 calculateMenu.addSeparator();
2360 calculateMenu.add(pairwiseAlignmentMenuItem);
2361 calculateMenu.add(PCAMenuItem);
2362 calculateMenu.addSeparator();
2363 calculateMenu.add(showTranslation);
2364 calculateMenu.add(showProducts);
2365 calculateMenu.add(autoCalculate);
2366 calculateMenu.add(sortByTree);
2367 calculateMenu.addSeparator();
2368 calculateMenu.add(extractScores);
2369 webServiceNoServices = new JMenuItem(
2370 MessageManager.getString("label.no_services"));
2371 webService.add(webServiceNoServices);
2372 pasteMenu.add(pasteNew);
2373 pasteMenu.add(pasteThis);
2374 sort.add(sortIDMenuItem);
2375 sort.add(sortLengthMenuItem);
2376 sort.add(sortGroupMenuItem);
2377 sort.add(sortPairwiseMenuItem);
2378 sort.add(sortByTreeMenu);
2379 jMenu2.add(htmlMenuItem);
2380 jMenu2.add(epsFile);
2381 jMenu2.add(createPNG);
2382 jMenu2.add(createBioJS);
2383 jMenu2.add(createSVG);
2384 addSequenceMenu.add(addFromFile);
2385 addSequenceMenu.add(addFromText);
2386 addSequenceMenu.add(addFromURL);
2387 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2388 statusPanel.add(statusBar, null);
2389 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2390 jMenu3.add(showAllColumns);
2391 jMenu3.add(showAllSeqs);
2392 jMenu3.add(showAllhidden);
2393 hideMenu.add(hideSelColumns);
2394 hideMenu.add(hideSelSequences);
2395 hideMenu.add(hideAllSelection);
2396 hideMenu.add(hideAllButSelection);
2398 formatMenu.add(font);
2399 formatMenu.addSeparator();
2400 formatMenu.add(wrapMenuItem);
2401 formatMenu.add(scaleAbove);
2402 formatMenu.add(scaleLeft);
2403 formatMenu.add(scaleRight);
2404 formatMenu.add(seqLimits);
2405 formatMenu.add(idRightAlign);
2406 formatMenu.add(hiddenMarkers);
2407 formatMenu.add(viewBoxesMenuItem);
2408 formatMenu.add(viewTextMenuItem);
2409 formatMenu.add(colourTextMenuItem);
2410 formatMenu.add(renderGapsMenuItem);
2411 formatMenu.add(centreColumnLabelsMenuItem);
2412 formatMenu.add(showNonconservedMenuItem);
2413 selectMenu.add(findMenuItem);
2414 selectMenu.addSeparator();
2415 selectMenu.add(selectAllSequenceMenuItem);
2416 selectMenu.add(deselectAllSequenceMenuItem);
2417 selectMenu.add(invertSequenceMenuItem);
2418 selectMenu.add(invertColSel);
2419 selectMenu.add(createGroup);
2420 selectMenu.add(unGroup);
2421 selectMenu.add(grpsFromSelection);
2422 selectMenu.add(deleteGroups);
2423 selectMenu.add(annotationColumn);
2424 calculateMenu.add(expandAlignment);
2425 // TODO - determine if the listenToViewSelections button is needed : see bug
2427 // selectMenu.addSeparator();
2428 // selectMenu.add(listenToViewSelections);
2432 * Action on clicking sort annotations by type.
2436 protected void sortAnnotations_actionPerformed()
2441 * Action on clicking Show all annotations.
2443 * @param forSequences
2444 * update sequence-related annotations
2445 * @param forAlignment
2446 * update non-sequence-related annotations
2448 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2449 boolean forAlignment)
2451 setAnnotationsVisibility(true, forSequences, forAlignment);
2455 * Action on clicking Hide all annotations.
2457 * @param forSequences
2458 * update sequence-related annotations
2459 * @param forAlignment
2460 * update non-sequence-related annotations
2462 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2463 boolean forAlignment)
2465 setAnnotationsVisibility(false, forSequences, forAlignment);
2469 * Set the visibility of annotations to true or false. Can act on
2470 * sequence-related annotations, or alignment-related, or both.
2473 * @param forSequences
2474 * update sequence-related annotations
2475 * @param forAlignment
2476 * update non-sequence-related annotations
2478 protected void setAnnotationsVisibility(boolean visible,
2479 boolean forSequences, boolean forAlignment)
2484 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2486 // TODO Auto-generated method stub
2490 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2492 // TODO Auto-generated method stub
2496 protected void showAllhidden_actionPerformed(ActionEvent e)
2498 // TODO Auto-generated method stub
2502 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2504 // TODO Auto-generated method stub
2508 protected void hideAllSelection_actionPerformed(ActionEvent e)
2510 // TODO Auto-generated method stub
2514 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2516 // TODO Auto-generated method stub
2520 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2522 // TODO Auto-generated method stub
2526 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2528 // TODO Auto-generated method stub
2532 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2534 // TODO Auto-generated method stub
2538 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2540 // TODO Auto-generated method stub
2544 protected void showGroupConservation_actionPerformed(ActionEvent e)
2546 // TODO Auto-generated method stub
2550 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2552 // TODO Auto-generated method stub
2556 protected void showSeqFeaturesHeight_actionPerformed(
2557 ActionEvent actionEvent)
2559 // TODO Auto-generated method stub
2563 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2565 // TODO Auto-generated method stub
2569 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2571 // TODO Auto-generated method stub
2575 protected void followHighlight_actionPerformed()
2577 // TODO Auto-generated method stub
2581 protected void showNpFeats_actionPerformed(ActionEvent e)
2583 // TODO Auto-generated method stub
2587 protected void showDbRefs_actionPerformed(ActionEvent e)
2589 // TODO Auto-generated method stub
2593 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2597 protected void showProducts_actionPerformed(ActionEvent e)
2601 protected void buildSortByAnnotationScoresMenu()
2605 protected void extractScores_actionPerformed(ActionEvent e)
2609 protected void outputText_actionPerformed(ActionEvent e)
2613 public void addFromFile_actionPerformed(ActionEvent e)
2618 public void addFromText_actionPerformed(ActionEvent e)
2623 public void addFromURL_actionPerformed(ActionEvent e)
2628 public void exportFeatures_actionPerformed(ActionEvent e)
2633 public void exportAnnotations_actionPerformed(ActionEvent e)
2638 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2642 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2647 protected void closeMenuItem_actionPerformed(boolean b)
2651 protected void redoMenuItem_actionPerformed(ActionEvent e)
2655 protected void undoMenuItem_actionPerformed(ActionEvent e)
2659 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2663 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2667 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2671 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2675 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2679 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2683 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2687 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2691 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2695 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2699 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2703 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2707 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2711 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2715 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2719 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2723 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2727 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2731 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2735 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2739 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2743 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2747 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2751 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2755 protected void clustalColour_actionPerformed(ActionEvent e)
2759 protected void zappoColour_actionPerformed(ActionEvent e)
2763 protected void taylorColour_actionPerformed(ActionEvent e)
2767 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2771 protected void helixColour_actionPerformed(ActionEvent e)
2775 protected void strandColour_actionPerformed(ActionEvent e)
2779 protected void turnColour_actionPerformed(ActionEvent e)
2783 protected void buriedColour_actionPerformed(ActionEvent e)
2787 protected void userDefinedColour_actionPerformed(ActionEvent e)
2791 protected void PIDColour_actionPerformed(ActionEvent e)
2795 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2799 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2803 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2808 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2811 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2815 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2819 protected void printMenuItem_actionPerformed(ActionEvent e)
2823 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2827 protected void findMenuItem_actionPerformed(ActionEvent e)
2831 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2835 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2839 protected void nucleotideColour_actionPerformed(ActionEvent e)
2843 protected void deleteGroups_actionPerformed(ActionEvent e)
2847 protected void createGroup_actionPerformed(ActionEvent e)
2851 protected void unGroup_actionPerformed(ActionEvent e)
2855 protected void copy_actionPerformed(ActionEvent e)
2859 protected void cut_actionPerformed(ActionEvent e)
2863 protected void delete_actionPerformed(ActionEvent e)
2867 protected void pasteNew_actionPerformed(ActionEvent e)
2871 protected void pasteThis_actionPerformed(ActionEvent e)
2875 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2879 public void createPNG(java.io.File f)
2883 protected void font_actionPerformed(ActionEvent e)
2887 protected void seqLimit_actionPerformed(ActionEvent e)
2891 public void seqDBRef_actionPerformed(ActionEvent e)
2896 public void createEPS(java.io.File f)
2900 public void createSVG(java.io.File f)
2904 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2910 * Template method to handle the 'load T-Coffee scores' menu event.
2912 * Subclasses override this method to provide a custom action.
2917 protected void loadScores_actionPerformed(ActionEvent event)
2923 * Template method to handle the 'Color T-Coffee scores' menu event.
2925 * Subclasses override this method to provide a custom action.
2930 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2935 protected void jpred_actionPerformed(ActionEvent e)
2939 protected void scaleAbove_actionPerformed(ActionEvent e)
2943 protected void scaleLeft_actionPerformed(ActionEvent e)
2947 protected void scaleRight_actionPerformed(ActionEvent e)
2951 protected void modifyPID_actionPerformed(ActionEvent e)
2955 protected void modifyConservation_actionPerformed(ActionEvent e)
2959 protected void saveAs_actionPerformed(ActionEvent e)
2963 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2967 public void vamsasStore_actionPerformed(ActionEvent e)
2972 public void vamsasLoad_actionPerformed(ActionEvent e)
2977 public void showTranslation_actionPerformed(ActionEvent e)
2982 public void featureSettings_actionPerformed(ActionEvent e)
2987 public void fetchSequence_actionPerformed(ActionEvent e)
2992 public void smoothFont_actionPerformed(ActionEvent e)
2997 public void annotationColour_actionPerformed(ActionEvent e)
3002 public void annotationColumn_actionPerformed(ActionEvent e)
3007 public void rnahelicesColour_actionPerformed(ActionEvent e)
3012 public void associatedData_actionPerformed(ActionEvent e)
3017 public void autoCalculate_actionPerformed(ActionEvent e)
3022 public void sortByTreeOption_actionPerformed(ActionEvent e)
3027 public void showAllSeqs_actionPerformed(ActionEvent e)
3032 public void showAllColumns_actionPerformed(ActionEvent e)
3037 public void hideSelSequences_actionPerformed(ActionEvent e)
3042 public void hideSelColumns_actionPerformed(ActionEvent e)
3047 public void hiddenMarkers_actionPerformed(ActionEvent e)
3052 public void findPdbId_actionPerformed(ActionEvent e)
3057 public void enterPdbId_actionPerformed(ActionEvent e)
3062 public void pdbFile_actionPerformed(ActionEvent e)
3067 public void invertColSel_actionPerformed(ActionEvent e)
3072 public void tabSelectionChanged(int sel)
3077 public void tabbedPane_mousePressed(MouseEvent e)
3082 public void tabbedPane_focusGained(FocusEvent e)
3087 public void save_actionPerformed(ActionEvent e)
3092 public void reload_actionPerformed(ActionEvent e)
3097 public void newView_actionPerformed(ActionEvent e)
3102 public void textColour_actionPerformed(ActionEvent e)
3107 public void idRightAlign_actionPerformed(ActionEvent e)
3112 public void expandViews_actionPerformed(ActionEvent e)
3117 public void gatherViews_actionPerformed(ActionEvent e)
3122 public void buildTreeMenu()
3127 public void pageSetup_actionPerformed(ActionEvent e)
3132 public void alignmentProperties()
3137 protected void expand_newalign(ActionEvent e)
3139 // TODO Auto-generated method stub
3143 protected boolean isShowAutoCalculatedAbove()
3145 return showAutoCalculatedAbove;
3148 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3150 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3153 protected SequenceAnnotationOrder getAnnotationSortOrder()
3155 return annotationSortOrder;
3158 protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
3160 this.annotationSortOrder = annotationSortOrder;