2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.jbgui;
21 import jalview.schemes.ColourSchemeProperty;
22 import jalview.util.MessageManager;
24 import java.awt.BorderLayout;
25 import java.awt.Color;
26 import java.awt.GridLayout;
27 import java.awt.Toolkit;
28 import java.awt.event.ActionEvent;
29 import java.awt.event.ActionListener;
30 import java.awt.event.FocusAdapter;
31 import java.awt.event.FocusEvent;
32 import java.awt.event.MouseAdapter;
33 import java.awt.event.MouseEvent;
35 import javax.swing.BorderFactory;
36 import javax.swing.ButtonGroup;
37 import javax.swing.JCheckBoxMenuItem;
38 import javax.swing.JInternalFrame;
39 import javax.swing.JLabel;
40 import javax.swing.JMenu;
41 import javax.swing.JMenuBar;
42 import javax.swing.JMenuItem;
43 import javax.swing.JOptionPane;
44 import javax.swing.JPanel;
45 import javax.swing.JRadioButtonMenuItem;
46 import javax.swing.JTabbedPane;
47 import javax.swing.SwingUtilities;
48 import javax.swing.event.ChangeEvent;
49 import javax.swing.event.MenuEvent;
50 import javax.swing.event.MenuListener;
52 public class GAlignFrame extends JInternalFrame
54 protected JMenuBar alignFrameMenuBar = new JMenuBar();
56 protected JMenu fileMenu = new JMenu();
58 protected JMenuItem closeMenuItem = new JMenuItem();
60 protected JMenu editMenu = new JMenu();
62 protected JMenu viewMenu = new JMenu();
64 protected JMenu colourMenu = new JMenu();
66 protected JMenu calculateMenu = new JMenu();
68 protected JMenu webService = new JMenu();
70 protected JMenuItem webServiceNoServices;
72 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
74 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
76 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
78 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
80 protected JMenuItem remove2RightMenuItem = new JMenuItem();
82 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
84 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
86 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
88 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
90 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
92 protected JMenuItem sortIDMenuItem = new JMenuItem();
94 protected JMenuItem sortLengthMenuItem = new JMenuItem();
96 protected JMenuItem sortGroupMenuItem = new JMenuItem();
98 protected JMenu sortByAnnotScore = new JMenu();
100 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
102 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
104 protected JMenuItem PCAMenuItem = new JMenuItem();
106 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
108 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
110 BorderLayout borderLayout1 = new BorderLayout();
112 public JLabel statusBar = new JLabel();
114 protected JMenuItem saveAs = new JMenuItem();
116 protected JMenu outputTextboxMenu = new JMenu();
118 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
120 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
122 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
124 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
126 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
128 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
130 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
132 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
134 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
136 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
138 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
140 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
142 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
144 // protected JRadioButtonMenuItem covariationColour = new
145 // JRadioButtonMenuItem();
147 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
149 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
151 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
153 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
155 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
157 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
159 JMenuItem htmlMenuItem = new JMenuItem();
161 JMenuItem overviewMenuItem = new JMenuItem();
163 protected JMenuItem undoMenuItem = new JMenuItem();
165 protected JMenuItem redoMenuItem = new JMenuItem();
167 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
169 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
171 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
173 JMenuItem printMenuItem = new JMenuItem();
175 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
177 JMenuItem findMenuItem = new JMenuItem();
179 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
181 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
183 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
185 JMenuItem deleteGroups = new JMenuItem();
187 JMenuItem createGroup = new JMenuItem();
188 JMenuItem unGroup = new JMenuItem();
190 JMenuItem delete = new JMenuItem();
192 JMenuItem copy = new JMenuItem();
194 JMenuItem cut = new JMenuItem();
196 JMenu pasteMenu = new JMenu();
198 JMenuItem pasteNew = new JMenuItem();
200 JMenuItem pasteThis = new JMenuItem();
202 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
204 JMenuItem createPNG = new JMenuItem();
206 protected JMenuItem font = new JMenuItem();
208 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
210 JMenuItem epsFile = new JMenuItem();
212 JMenuItem LoadtreeMenuItem = new JMenuItem();
214 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
216 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
218 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
220 protected JMenuItem modifyPID = new JMenuItem();
222 protected JMenuItem modifyConservation = new JMenuItem();
224 protected JMenu sortByTreeMenu = new JMenu();
226 protected JMenu sort = new JMenu();
228 protected JMenu calculateTree = new JMenu();
230 JMenu jMenu2 = new JMenu();
232 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
234 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
236 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
238 protected ButtonGroup colours = new ButtonGroup();
240 JMenuItem vamsasStore = new JMenuItem();
242 protected JMenuItem showTranslation = new JMenuItem();
244 protected JMenuItem extractScores = new JMenuItem();
246 protected JMenu showProducts = new JMenu();
248 public JMenuItem openFeatureSettings = new JMenuItem();
250 JMenuItem fetchSequence = new JMenuItem();
252 JMenuItem annotationColour = new JMenuItem();
254 protected JMenuItem rnahelicesColour = new JMenuItem();
256 JMenuItem associatedData = new JMenuItem();
258 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
260 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
262 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
264 JMenu addSequenceMenu = new JMenu();
266 JMenuItem addFromFile = new JMenuItem();
268 JMenuItem addFromText = new JMenuItem();
270 JMenuItem addFromURL = new JMenuItem();
272 JMenuItem exportAnnotations = new JMenuItem();
274 JMenuItem exportFeatures = new JMenuItem();
276 protected JPanel statusPanel = new JPanel();
278 GridLayout gridLayout1 = new GridLayout();
280 JMenu jMenu3 = new JMenu();
282 JMenuItem showAllSeqs = new JMenuItem();
284 JMenuItem showAllColumns = new JMenuItem();
286 JMenu hideMenu = new JMenu();
288 JMenuItem hideSelSequences = new JMenuItem();
290 JMenuItem hideSelColumns = new JMenuItem();
292 JMenuItem hideAllButSelection = new JMenuItem();
294 JMenuItem hideAllSelection = new JMenuItem();
296 JMenuItem showAllhidden = new JMenuItem();
298 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
300 JMenuItem invertColSel = new JMenuItem();
302 protected JTabbedPane tabbedPane = new JTabbedPane();
304 JMenuItem save = new JMenuItem();
306 protected JMenuItem reload = new JMenuItem();
308 JMenuItem newView = new JMenuItem();
310 JMenuItem textColour = new JMenuItem();
312 JMenu formatMenu = new JMenu();
314 JMenu selectMenu = new JMenu();
316 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
318 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
320 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
322 protected JMenuItem gatherViews = new JMenuItem();
324 protected JMenuItem expandViews = new JMenuItem();
326 JMenuItem pageSetup = new JMenuItem();
328 JMenuItem alignmentProperties = new JMenuItem();
330 JMenu tooltipSettingsMenu = new JMenu();
332 private JMenuItem justifyLeftMenuItem = new JMenuItem();
334 private JMenuItem justifyRightMenuItem = new JMenuItem();
336 JMenu autoAnnMenu = new JMenu();
338 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
340 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
342 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
344 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
346 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
348 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
350 private JMenuItem grpsFromSelection = new JMenuItem();
357 setJMenuBar(alignFrameMenuBar);
359 // dynamically fill save as menu with available formats
360 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
362 JMenuItem item = new JMenuItem(
363 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
365 item.addActionListener(new java.awt.event.ActionListener()
367 public void actionPerformed(ActionEvent e)
369 outputText_actionPerformed(e);
373 outputTextboxMenu.add(item);
375 } catch (Exception e)
379 if (!new jalview.util.Platform().isAMac())
381 closeMenuItem.setMnemonic('C');
382 outputTextboxMenu.setMnemonic('T');
383 undoMenuItem.setMnemonic('Z');
384 redoMenuItem.setMnemonic('0');
385 copy.setMnemonic('C');
386 cut.setMnemonic('U');
387 pasteMenu.setMnemonic('P');
388 reload.setMnemonic('R');
391 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
393 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
394 .getUserColourSchemes().keys();
396 while (userColours.hasMoreElements())
398 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
399 userColours.nextElement().toString());
400 radioItem.setName("USER_DEFINED");
401 radioItem.addMouseListener(new MouseAdapter()
403 public void mousePressed(MouseEvent evt)
405 if (evt.isControlDown()
406 || SwingUtilities.isRightMouseButton(evt))
408 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
410 int option = JOptionPane.showInternalConfirmDialog(
411 jalview.gui.Desktop.desktop,
412 MessageManager.getString("label.remove_from_default_list"),
413 MessageManager.getString("label.remove_user_defined_colour"),
414 JOptionPane.YES_NO_OPTION);
415 if (option == JOptionPane.YES_OPTION)
417 jalview.gui.UserDefinedColours
418 .removeColourFromDefaults(radioItem.getText());
419 colourMenu.remove(radioItem);
423 radioItem.addActionListener(new ActionListener()
425 public void actionPerformed(ActionEvent evt)
427 userDefinedColour_actionPerformed(evt);
434 radioItem.addActionListener(new ActionListener()
436 public void actionPerformed(ActionEvent evt)
438 userDefinedColour_actionPerformed(evt);
441 colourMenu.insert(radioItem, 15);
442 colours.add(radioItem);
445 colours.add(noColourmenuItem);
446 colours.add(clustalColour);
447 colours.add(zappoColour);
448 colours.add(taylorColour);
449 colours.add(hydrophobicityColour);
450 colours.add(helixColour);
451 colours.add(strandColour);
452 colours.add(turnColour);
453 colours.add(buriedColour);
454 colours.add(userDefinedColour);
455 colours.add(PIDColour);
456 colours.add(BLOSUM62Colour);
457 colours.add(nucleotideColour);
458 colours.add(purinePyrimidineColour);
459 // colours.add(covariationColour);
460 colours.add(tcoffeeColour);
462 setColourSelected(jalview.bin.Cache
463 .getDefault("DEFAULT_COLOUR", "None"));
467 public void setColourSelected(String defaultColour)
470 if (defaultColour != null)
472 int index = ColourSchemeProperty
473 .getColourIndexFromName(defaultColour);
477 case ColourSchemeProperty.CLUSTAL:
478 clustalColour.setSelected(true);
482 case ColourSchemeProperty.BLOSUM:
483 BLOSUM62Colour.setSelected(true);
487 case ColourSchemeProperty.PID:
488 PIDColour.setSelected(true);
492 case ColourSchemeProperty.ZAPPO:
493 zappoColour.setSelected(true);
497 case ColourSchemeProperty.TAYLOR:
498 taylorColour.setSelected(true);
501 case ColourSchemeProperty.HYDROPHOBIC:
502 hydrophobicityColour.setSelected(true);
506 case ColourSchemeProperty.HELIX:
507 helixColour.setSelected(true);
511 case ColourSchemeProperty.STRAND:
512 strandColour.setSelected(true);
516 case ColourSchemeProperty.TURN:
517 turnColour.setSelected(true);
521 case ColourSchemeProperty.BURIED:
522 buriedColour.setSelected(true);
526 case ColourSchemeProperty.NUCLEOTIDE:
527 nucleotideColour.setSelected(true);
531 case ColourSchemeProperty.TCOFFEE:
532 tcoffeeColour.setSelected(true);
535 case ColourSchemeProperty.PURINEPYRIMIDINE:
536 purinePyrimidineColour.setSelected(true);
540 * case ColourSchemeProperty.COVARIATION:
541 * covariationColour.setSelected(true);
545 case ColourSchemeProperty.USER_DEFINED:
546 userDefinedColour.setSelected(true);
549 case ColourSchemeProperty.NONE:
551 noColourmenuItem.setSelected(true);
559 private void jbInit() throws Exception
561 fileMenu.setText(MessageManager.getString("action.file"));
562 saveAs.setText(MessageManager.getString("action.save_as") + "...");
563 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
564 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
565 .getMenuShortcutKeyMask()
566 | java.awt.event.KeyEvent.SHIFT_MASK, false));
567 saveAs.addActionListener(new ActionListener()
569 public void actionPerformed(ActionEvent e)
571 saveAs_actionPerformed(e);
574 closeMenuItem.setText(MessageManager.getString("action.close"));
575 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
576 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
577 .getMenuShortcutKeyMask(), false));
578 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
580 public void actionPerformed(ActionEvent e)
582 closeMenuItem_actionPerformed(false);
585 editMenu.setText(MessageManager.getString("action.edit"));
586 viewMenu.setText(MessageManager.getString("action.view"));
587 colourMenu.setText(MessageManager.getString("action.colour"));
588 calculateMenu.setText(MessageManager.getString("action.calculate"));
589 webService.setText(MessageManager.getString("action.web_service"));
590 selectAllSequenceMenuItem.setText(MessageManager.getString("action.select_all"));
591 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
592 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
593 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
594 selectAllSequenceMenuItem
595 .addActionListener(new java.awt.event.ActionListener()
597 public void actionPerformed(ActionEvent e)
599 selectAllSequenceMenuItem_actionPerformed(e);
602 deselectAllSequenceMenuItem.setText(MessageManager.getString("action.deselect_all"));
603 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
604 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
605 deselectAllSequenceMenuItem
606 .addActionListener(new java.awt.event.ActionListener()
608 public void actionPerformed(ActionEvent e)
610 deselectAllSequenceMenuItem_actionPerformed(e);
613 invertSequenceMenuItem.setText(MessageManager.getString("action.invert_sequence_selection"));
614 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
615 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
616 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
617 invertSequenceMenuItem
618 .addActionListener(new java.awt.event.ActionListener()
620 public void actionPerformed(ActionEvent e)
622 invertSequenceMenuItem_actionPerformed(e);
625 grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
626 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
628 public void actionPerformed(ActionEvent e)
630 makeGrpsFromSelection_actionPerformed(e);
634 remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
635 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
636 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
637 .getMenuShortcutKeyMask(), false));
639 .addActionListener(new java.awt.event.ActionListener()
641 public void actionPerformed(ActionEvent e)
643 remove2LeftMenuItem_actionPerformed(e);
646 remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
647 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
648 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
649 .getMenuShortcutKeyMask(), false));
651 .addActionListener(new java.awt.event.ActionListener()
653 public void actionPerformed(ActionEvent e)
655 remove2RightMenuItem_actionPerformed(e);
658 removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
659 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
660 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
661 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
662 removeGappedColumnMenuItem
663 .addActionListener(new java.awt.event.ActionListener()
665 public void actionPerformed(ActionEvent e)
667 removeGappedColumnMenuItem_actionPerformed(e);
670 removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
671 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
672 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
673 .getDefaultToolkit().getMenuShortcutKeyMask()
674 | java.awt.event.KeyEvent.SHIFT_MASK, false));
675 removeAllGapsMenuItem
676 .addActionListener(new java.awt.event.ActionListener()
678 public void actionPerformed(ActionEvent e)
680 removeAllGapsMenuItem_actionPerformed(e);
683 justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
685 .addActionListener(new java.awt.event.ActionListener()
687 public void actionPerformed(ActionEvent e)
689 justifyLeftMenuItem_actionPerformed(e);
692 justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
694 .addActionListener(new java.awt.event.ActionListener()
696 public void actionPerformed(ActionEvent e)
698 justifyRightMenuItem_actionPerformed(e);
701 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
702 viewBoxesMenuItem.setState(true);
703 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
705 public void actionPerformed(ActionEvent e)
707 viewBoxesMenuItem_actionPerformed(e);
710 viewTextMenuItem.setText(MessageManager.getString("action.text"));
711 viewTextMenuItem.setState(true);
712 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
714 public void actionPerformed(ActionEvent e)
716 viewTextMenuItem_actionPerformed(e);
719 showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
720 showNonconservedMenuItem.setState(false);
721 showNonconservedMenuItem
722 .addActionListener(new java.awt.event.ActionListener()
724 public void actionPerformed(ActionEvent e)
726 showUnconservedMenuItem_actionPerformed(e);
729 sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
731 .addActionListener(new java.awt.event.ActionListener()
733 public void actionPerformed(ActionEvent e)
735 sortPairwiseMenuItem_actionPerformed(e);
738 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
739 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
741 public void actionPerformed(ActionEvent e)
743 sortIDMenuItem_actionPerformed(e);
746 sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
748 .addActionListener(new java.awt.event.ActionListener()
750 public void actionPerformed(ActionEvent e)
752 sortLengthMenuItem_actionPerformed(e);
755 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
756 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
758 public void actionPerformed(ActionEvent e)
760 sortGroupMenuItem_actionPerformed(e);
763 removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
764 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
765 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
766 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
767 removeRedundancyMenuItem
768 .addActionListener(new java.awt.event.ActionListener()
770 public void actionPerformed(ActionEvent e)
772 removeRedundancyMenuItem_actionPerformed(e);
775 pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
776 pairwiseAlignmentMenuItem
777 .addActionListener(new java.awt.event.ActionListener()
779 public void actionPerformed(ActionEvent e)
781 pairwiseAlignmentMenuItem_actionPerformed(e);
784 PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
785 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
787 public void actionPerformed(ActionEvent e)
789 PCAMenuItem_actionPerformed(e);
792 averageDistanceTreeMenuItem
793 .setText(MessageManager.getString("label.average_distance_identity"));
794 averageDistanceTreeMenuItem
795 .addActionListener(new java.awt.event.ActionListener()
797 public void actionPerformed(ActionEvent e)
799 averageDistanceTreeMenuItem_actionPerformed(e);
802 neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
803 neighbourTreeMenuItem
804 .addActionListener(new java.awt.event.ActionListener()
806 public void actionPerformed(ActionEvent e)
808 neighbourTreeMenuItem_actionPerformed(e);
811 this.getContentPane().setLayout(borderLayout1);
812 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
813 statusBar.setBackground(Color.white);
814 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
815 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
816 statusBar.setText(MessageManager.getString("label.status_bar"));
817 outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
818 clustalColour.setText(MessageManager.getString("label.clustalx"));
820 clustalColour.addActionListener(new java.awt.event.ActionListener()
822 public void actionPerformed(ActionEvent e)
824 clustalColour_actionPerformed(e);
827 zappoColour.setText(MessageManager.getString("label.zappo"));
828 zappoColour.addActionListener(new java.awt.event.ActionListener()
830 public void actionPerformed(ActionEvent e)
832 zappoColour_actionPerformed(e);
835 taylorColour.setText(MessageManager.getString("label.taylor"));
836 taylorColour.addActionListener(new java.awt.event.ActionListener()
838 public void actionPerformed(ActionEvent e)
840 taylorColour_actionPerformed(e);
843 hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
845 .addActionListener(new java.awt.event.ActionListener()
847 public void actionPerformed(ActionEvent e)
849 hydrophobicityColour_actionPerformed(e);
852 helixColour.setText(MessageManager.getString("label.helix_propensity"));
853 helixColour.addActionListener(new java.awt.event.ActionListener()
855 public void actionPerformed(ActionEvent e)
857 helixColour_actionPerformed(e);
860 strandColour.setText(MessageManager.getString("label.strand_propensity"));
861 strandColour.addActionListener(new java.awt.event.ActionListener()
863 public void actionPerformed(ActionEvent e)
865 strandColour_actionPerformed(e);
868 turnColour.setText(MessageManager.getString("Turn Propensity"));
869 turnColour.addActionListener(new java.awt.event.ActionListener()
871 public void actionPerformed(ActionEvent e)
873 turnColour_actionPerformed(e);
876 buriedColour.setText(MessageManager.getString("Buried Index"));
877 buriedColour.addActionListener(new java.awt.event.ActionListener()
879 public void actionPerformed(ActionEvent e)
881 buriedColour_actionPerformed(e);
884 userDefinedColour.setText(MessageManager.getString("action.user_defined"));
885 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
887 public void actionPerformed(ActionEvent e)
889 userDefinedColour_actionPerformed(e);
892 PIDColour.setText(MessageManager.getString("label.percentage_identity"));
893 PIDColour.addActionListener(new java.awt.event.ActionListener()
895 public void actionPerformed(ActionEvent e)
897 PIDColour_actionPerformed(e);
900 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
901 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
903 public void actionPerformed(ActionEvent e)
905 BLOSUM62Colour_actionPerformed(e);
908 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
909 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
911 public void actionPerformed(ActionEvent e)
913 nucleotideColour_actionPerformed(e);
917 purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
918 purinePyrimidineColour
919 .addActionListener(new java.awt.event.ActionListener()
921 public void actionPerformed(ActionEvent e)
923 purinePyrimidineColour_actionPerformed(e);
927 * covariationColour.setText("Covariation");
928 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
929 * public void actionPerformed(ActionEvent e) {
930 * covariationColour_actionPerformed(e); } });
933 avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
934 avDistanceTreeBlosumMenuItem
935 .addActionListener(new java.awt.event.ActionListener()
937 public void actionPerformed(ActionEvent e)
939 avTreeBlosumMenuItem_actionPerformed(e);
942 njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
944 .addActionListener(new java.awt.event.ActionListener()
946 public void actionPerformed(ActionEvent e)
948 njTreeBlosumMenuItem_actionPerformed(e);
951 annotationPanelMenuItem.setActionCommand("");
952 annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
953 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
954 "SHOW_ANNOTATIONS", true));
955 annotationPanelMenuItem
956 .addActionListener(new java.awt.event.ActionListener()
958 public void actionPerformed(ActionEvent e)
960 annotationPanelMenuItem_actionPerformed(e);
963 colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
965 .addActionListener(new java.awt.event.ActionListener()
967 public void actionPerformed(ActionEvent e)
969 colourTextMenuItem_actionPerformed(e);
972 htmlMenuItem.setText(MessageManager.getString("label.html"));
973 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
975 public void actionPerformed(ActionEvent e)
977 htmlMenuItem_actionPerformed(e);
980 overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
981 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
983 public void actionPerformed(ActionEvent e)
985 overviewMenuItem_actionPerformed(e);
988 undoMenuItem.setEnabled(false);
989 undoMenuItem.setText(MessageManager.getString("action.undo"));
990 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
991 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
992 .getMenuShortcutKeyMask(), false));
993 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
995 public void actionPerformed(ActionEvent e)
997 undoMenuItem_actionPerformed(e);
1000 redoMenuItem.setEnabled(false);
1001 redoMenuItem.setText(MessageManager.getString("action.redo"));
1002 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1003 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1004 .getMenuShortcutKeyMask(), false));
1005 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1007 public void actionPerformed(ActionEvent e)
1009 redoMenuItem_actionPerformed(e);
1012 conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
1013 conservationMenuItem
1014 .addActionListener(new java.awt.event.ActionListener()
1016 public void actionPerformed(ActionEvent e)
1018 conservationMenuItem_actionPerformed(e);
1021 noColourmenuItem.setText(MessageManager.getString("label.none"));
1022 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1024 public void actionPerformed(ActionEvent e)
1026 noColourmenuItem_actionPerformed(e);
1029 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1030 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1032 public void actionPerformed(ActionEvent e)
1034 wrapMenuItem_actionPerformed(e);
1037 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1038 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1039 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1040 .getMenuShortcutKeyMask(), false));
1041 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1043 public void actionPerformed(ActionEvent e)
1045 printMenuItem_actionPerformed(e);
1048 renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
1049 renderGapsMenuItem.setState(true);
1051 .addActionListener(new java.awt.event.ActionListener()
1053 public void actionPerformed(ActionEvent e)
1055 renderGapsMenuItem_actionPerformed(e);
1058 findMenuItem.setText(MessageManager.getString("action.find"));
1059 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1060 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1061 .getMenuShortcutKeyMask(), false));
1062 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1064 public void actionPerformed(ActionEvent e)
1066 findMenuItem_actionPerformed(e);
1069 abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
1070 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1072 public void actionPerformed(ActionEvent e)
1074 abovePIDThreshold_actionPerformed(e);
1077 showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
1078 showSeqFeatures.addActionListener(new ActionListener()
1080 public void actionPerformed(ActionEvent actionEvent)
1082 showSeqFeatures_actionPerformed(actionEvent);
1086 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1087 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1088 * void actionPerformed(ActionEvent actionEvent) {
1089 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1091 showDbRefsMenuitem.setText(MessageManager.getString("label.show_database_refs"));
1092 showDbRefsMenuitem.addActionListener(new ActionListener()
1095 public void actionPerformed(ActionEvent e)
1097 showDbRefs_actionPerformed(e);
1101 showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
1102 showNpFeatsMenuitem.addActionListener(new ActionListener()
1105 public void actionPerformed(ActionEvent e)
1107 showNpFeats_actionPerformed(e);
1111 showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
1112 showGroupConservation.addActionListener(new ActionListener()
1115 public void actionPerformed(ActionEvent e)
1117 showGroupConservation_actionPerformed(e);
1122 showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
1123 showGroupConsensus.addActionListener(new ActionListener()
1126 public void actionPerformed(ActionEvent e)
1128 showGroupConsensus_actionPerformed(e);
1132 showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
1133 showConsensusHistogram.addActionListener(new ActionListener()
1136 public void actionPerformed(ActionEvent e)
1138 showConsensusHistogram_actionPerformed(e);
1142 showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
1143 showSequenceLogo.addActionListener(new ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 showSequenceLogo_actionPerformed(e);
1152 normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
1153 normaliseSequenceLogo.addActionListener(new ActionListener()
1156 public void actionPerformed(ActionEvent e)
1158 normaliseSequenceLogo_actionPerformed(e);
1162 applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
1163 applyAutoAnnotationSettings.setState(false);
1164 applyAutoAnnotationSettings.setVisible(true);
1165 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1168 public void actionPerformed(ActionEvent e)
1170 applyAutoAnnotationSettings_actionPerformed(e);
1175 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1176 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1178 public void actionPerformed(ActionEvent e)
1180 nucleotideColour_actionPerformed(e);
1184 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1185 tcoffeeColour.setEnabled(false);
1186 tcoffeeColour.addActionListener(new ActionListener()
1190 public void actionPerformed(ActionEvent e)
1192 tcoffeeColorScheme_actionPerformed(e);
1196 deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
1197 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1198 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1199 .getMenuShortcutKeyMask(), false));
1200 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1202 public void actionPerformed(ActionEvent e)
1204 deleteGroups_actionPerformed(e);
1207 createGroup.setText(MessageManager.getString("action.create_groups"));
1208 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1209 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1210 .getMenuShortcutKeyMask(), false));
1211 createGroup.addActionListener(new java.awt.event.ActionListener()
1213 public void actionPerformed(ActionEvent e)
1215 createGroup_actionPerformed(e);
1218 unGroup.setText(MessageManager.getString("action.remove_group"));
1219 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1220 java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
1221 .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
1222 unGroup.addActionListener(new java.awt.event.ActionListener()
1224 public void actionPerformed(ActionEvent e)
1226 unGroup_actionPerformed(e);
1229 copy.setText(MessageManager.getString("action.copy"));
1230 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1231 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1232 .getMenuShortcutKeyMask(), false));
1234 copy.addActionListener(new java.awt.event.ActionListener()
1236 public void actionPerformed(ActionEvent e)
1238 copy_actionPerformed(e);
1241 cut.setText(MessageManager.getString("action.cut"));
1242 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1243 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1244 .getMenuShortcutKeyMask(), false));
1245 cut.addActionListener(new java.awt.event.ActionListener()
1247 public void actionPerformed(ActionEvent e)
1249 cut_actionPerformed(e);
1252 delete.setText(MessageManager.getString("action.delete"));
1253 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1254 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1255 delete.addActionListener(new java.awt.event.ActionListener()
1257 public void actionPerformed(ActionEvent e)
1259 delete_actionPerformed(e);
1262 pasteMenu.setText(MessageManager.getString("action.paste"));
1263 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1264 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1265 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1266 .getMenuShortcutKeyMask()
1267 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1268 pasteNew.addActionListener(new java.awt.event.ActionListener()
1270 public void actionPerformed(ActionEvent e)
1272 pasteNew_actionPerformed(e);
1275 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1276 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1277 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1278 .getMenuShortcutKeyMask(), false));
1279 pasteThis.addActionListener(new java.awt.event.ActionListener()
1281 public void actionPerformed(ActionEvent e)
1283 pasteThis_actionPerformed(e);
1286 applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
1287 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1289 public void actionPerformed(ActionEvent e)
1291 applyToAllGroups_actionPerformed(e);
1294 createPNG.addActionListener(new java.awt.event.ActionListener()
1296 public void actionPerformed(ActionEvent e)
1301 createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
1302 createPNG.setText("PNG");
1303 font.setText(MessageManager.getString("action.font"));
1304 font.addActionListener(new java.awt.event.ActionListener()
1306 public void actionPerformed(ActionEvent e)
1308 font_actionPerformed(e);
1312 seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
1313 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1314 seqLimits.addActionListener(new java.awt.event.ActionListener()
1316 public void actionPerformed(ActionEvent e)
1318 seqLimit_actionPerformed(e);
1321 epsFile.setText("EPS");
1322 epsFile.addActionListener(new java.awt.event.ActionListener()
1324 public void actionPerformed(ActionEvent e)
1329 LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
1330 LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree"));
1331 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1333 public void actionPerformed(ActionEvent e)
1335 LoadtreeMenuItem_actionPerformed(e);
1339 scaleAbove.setVisible(false);
1340 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1341 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1343 public void actionPerformed(ActionEvent e)
1345 scaleAbove_actionPerformed(e);
1348 scaleLeft.setVisible(false);
1349 scaleLeft.setSelected(true);
1350 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1351 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1353 public void actionPerformed(ActionEvent e)
1355 scaleLeft_actionPerformed(e);
1358 scaleRight.setVisible(false);
1359 scaleRight.setSelected(true);
1360 scaleRight.setText(MessageManager.getString("action.scale_right"));
1361 scaleRight.addActionListener(new java.awt.event.ActionListener()
1363 public void actionPerformed(ActionEvent e)
1365 scaleRight_actionPerformed(e);
1368 centreColumnLabelsMenuItem.setVisible(true);
1369 centreColumnLabelsMenuItem.setState(false);
1370 centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
1371 centreColumnLabelsMenuItem
1372 .addActionListener(new java.awt.event.ActionListener()
1374 public void actionPerformed(ActionEvent e)
1376 centreColumnLabels_actionPerformed(e);
1379 followHighlightMenuItem.setVisible(true);
1380 followHighlightMenuItem.setState(true);
1381 followHighlightMenuItem.setText(MessageManager.getString("label.automatic_scrolling"));
1382 followHighlightMenuItem.addActionListener(new ActionListener()
1385 public void actionPerformed(ActionEvent e)
1387 followHighlight_actionPerformed();
1392 modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
1393 modifyPID.addActionListener(new java.awt.event.ActionListener()
1395 public void actionPerformed(ActionEvent e)
1397 modifyPID_actionPerformed(e);
1400 modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
1402 .addActionListener(new java.awt.event.ActionListener()
1404 public void actionPerformed(ActionEvent e)
1406 modifyConservation_actionPerformed(e);
1409 sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order"));
1410 sort.setText(MessageManager.getString("action.sort"));
1411 sort.addMenuListener(new MenuListener()
1413 public void menuSelected(MenuEvent e)
1418 public void menuDeselected(MenuEvent e)
1422 public void menuCanceled(MenuEvent e)
1426 sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
1427 sort.add(sortByAnnotScore);
1428 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1431 public void menuCanceled(MenuEvent e)
1435 public void menuDeselected(MenuEvent e)
1439 public void menuSelected(MenuEvent e)
1441 buildSortByAnnotationScoresMenu();
1444 sortByAnnotScore.setVisible(false);
1446 calculateTree.setText(MessageManager.getString("action.calculate_tree"));
1448 jMenu2.setText(MessageManager.getString("label.export_image"));
1449 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1450 padGapsMenuitem.setState(jalview.bin.Cache
1451 .getDefault("PAD_GAPS", false));
1452 padGapsMenuitem.addActionListener(new ActionListener()
1454 public void actionPerformed(ActionEvent e)
1456 padGapsMenuitem_actionPerformed(e);
1459 vamsasStore.setVisible(false);
1460 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1461 vamsasStore.addActionListener(new ActionListener()
1463 public void actionPerformed(ActionEvent e)
1465 vamsasStore_actionPerformed(e);
1468 showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
1469 showTranslation.addActionListener(new ActionListener()
1471 public void actionPerformed(ActionEvent e)
1473 showTranslation_actionPerformed(e);
1476 extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
1477 extractScores.addActionListener(new ActionListener()
1479 public void actionPerformed(ActionEvent e)
1481 extractScores_actionPerformed(e);
1484 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1486 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1488 * showProducts.addActionListener(new ActionListener() {
1490 * public void actionPerformed(ActionEvent e) {
1491 * showProducts_actionPerformed(e); } });
1493 openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
1494 openFeatureSettings.addActionListener(new ActionListener()
1496 public void actionPerformed(ActionEvent e)
1498 featureSettings_actionPerformed(e);
1501 fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
1502 fetchSequence.addActionListener(new ActionListener()
1504 public void actionPerformed(ActionEvent e)
1506 fetchSequence_actionPerformed(e);
1510 annotationColour.setText(MessageManager.getString("action.by_annotation"));
1511 annotationColour.addActionListener(new ActionListener()
1513 public void actionPerformed(ActionEvent e)
1515 annotationColour_actionPerformed(e);
1519 rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
1520 rnahelicesColour.addActionListener(new ActionListener()
1522 public void actionPerformed(ActionEvent e)
1524 rnahelicesColour_actionPerformed(e);
1528 associatedData.setText(MessageManager.getString("label.load_features_annotations"));
1529 associatedData.addActionListener(new ActionListener()
1531 public void actionPerformed(ActionEvent e)
1533 associatedData_actionPerformed(e);
1536 autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
1537 autoCalculate.setState(jalview.bin.Cache.getDefault(
1538 "AUTO_CALC_CONSENSUS", true));
1539 autoCalculate.addActionListener(new ActionListener()
1541 public void actionPerformed(ActionEvent e)
1543 autoCalculate_actionPerformed(e);
1546 sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
1548 .setToolTipText("<html>" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1550 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1551 sortByTree.addActionListener(new ActionListener()
1553 public void actionPerformed(ActionEvent e)
1555 sortByTreeOption_actionPerformed(e);
1559 listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
1560 listenToViewSelections
1561 .setToolTipText("<html>" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1562 listenToViewSelections.setState(false);
1563 listenToViewSelections.addActionListener(new ActionListener()
1565 public void actionPerformed(ActionEvent e)
1567 listenToViewSelections_actionPerformed(e);
1571 addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
1572 addFromFile.setText(MessageManager.getString("label.from_file"));
1573 addFromFile.addActionListener(new ActionListener()
1575 public void actionPerformed(ActionEvent e)
1577 addFromFile_actionPerformed(e);
1580 addFromText.setText(MessageManager.getString("label.from_textbox"));
1581 addFromText.addActionListener(new ActionListener()
1583 public void actionPerformed(ActionEvent e)
1585 addFromText_actionPerformed(e);
1588 addFromURL.setText(MessageManager.getString("label.from_url"));
1589 addFromURL.addActionListener(new ActionListener()
1591 public void actionPerformed(ActionEvent e)
1593 addFromURL_actionPerformed(e);
1596 exportFeatures.setText(MessageManager.getString("label.export_features"));
1597 exportFeatures.addActionListener(new ActionListener()
1599 public void actionPerformed(ActionEvent e)
1601 exportFeatures_actionPerformed(e);
1604 exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
1605 exportAnnotations.addActionListener(new ActionListener()
1607 public void actionPerformed(ActionEvent e)
1609 exportAnnotations_actionPerformed(e);
1612 statusPanel.setLayout(gridLayout1);
1613 jMenu3.setText(MessageManager.getString("action.show"));
1614 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1615 showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1616 showAllSeqs.addActionListener(new ActionListener()
1618 public void actionPerformed(ActionEvent e)
1620 showAllSeqs_actionPerformed(e);
1623 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1624 showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1625 showAllColumns.addActionListener(new ActionListener()
1627 public void actionPerformed(ActionEvent e)
1629 showAllColumns_actionPerformed(e);
1632 hideMenu.setText(MessageManager.getString("action.hide"));
1633 hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
1634 hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1635 hideSelSequences.addActionListener(new ActionListener()
1637 public void actionPerformed(ActionEvent e)
1639 hideSelSequences_actionPerformed(e);
1642 hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
1643 hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1644 hideSelColumns.addActionListener(new ActionListener()
1646 public void actionPerformed(ActionEvent e)
1648 hideSelColumns_actionPerformed(e);
1651 hideAllSelection.setText(MessageManager.getString("label.selected_region"));
1652 hideAllSelection.addActionListener(new ActionListener()
1654 public void actionPerformed(ActionEvent e)
1656 hideAllSelection_actionPerformed(e);
1659 // TODO: should be hidden if no selection exists.
1660 hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
1661 hideAllButSelection.addActionListener(new ActionListener()
1663 public void actionPerformed(ActionEvent e)
1665 hideAllButSelection_actionPerformed(e);
1668 showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
1670 .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
1671 showAllhidden.addActionListener(new ActionListener()
1673 public void actionPerformed(ActionEvent e)
1675 showAllhidden_actionPerformed(e);
1679 hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
1680 hiddenMarkers.addActionListener(new ActionListener()
1682 public void actionPerformed(ActionEvent e)
1684 hiddenMarkers_actionPerformed(e);
1687 invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
1688 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1689 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1690 .getMenuShortcutKeyMask()
1691 | java.awt.event.KeyEvent.ALT_MASK, false));
1692 invertColSel.addActionListener(new ActionListener()
1694 public void actionPerformed(ActionEvent e)
1696 invertColSel_actionPerformed(e);
1699 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1701 public void stateChanged(ChangeEvent evt)
1703 JTabbedPane pane = (JTabbedPane) evt.getSource();
1704 int sel = pane.getSelectedIndex();
1705 tabSelectionChanged(sel);
1708 tabbedPane.addMouseListener(new MouseAdapter()
1710 public void mousePressed(MouseEvent e)
1712 tabbedPane_mousePressed(e);
1715 tabbedPane.addFocusListener(new FocusAdapter()
1717 public void focusGained(FocusEvent e)
1719 tabbedPane_focusGained(e);
1722 save.setText(MessageManager.getString("action.save"));
1723 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1724 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1725 .getMenuShortcutKeyMask(), false));
1726 save.addActionListener(new ActionListener()
1728 public void actionPerformed(ActionEvent e)
1730 save_actionPerformed(e);
1733 reload.setEnabled(false);
1734 reload.setText(MessageManager.getString("action.reload"));
1735 reload.addActionListener(new ActionListener()
1737 public void actionPerformed(ActionEvent e)
1739 reload_actionPerformed(e);
1742 newView.setText(MessageManager.getString("action.new_view"));
1743 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1744 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1745 .getMenuShortcutKeyMask(), false));
1746 newView.addActionListener(new ActionListener()
1748 public void actionPerformed(ActionEvent e)
1750 newView_actionPerformed(e);
1753 tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
1754 textColour.setText(MessageManager.getString("label.colour_text") + "...");
1755 textColour.addActionListener(new ActionListener()
1757 public void actionPerformed(ActionEvent e)
1759 textColour_actionPerformed(e);
1762 formatMenu.setText(MessageManager.getString("action.format"));
1763 selectMenu.setText(MessageManager.getString("action.select"));
1764 idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id"));
1765 idRightAlign.addActionListener(new ActionListener()
1767 public void actionPerformed(ActionEvent e)
1769 idRightAlign_actionPerformed(e);
1772 gatherViews.setEnabled(false);
1773 gatherViews.setText(MessageManager.getString("action.gather_views"));
1774 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1775 java.awt.event.KeyEvent.VK_G, 0, false));
1776 gatherViews.addActionListener(new ActionListener()
1778 public void actionPerformed(ActionEvent e)
1780 gatherViews_actionPerformed(e);
1783 expandViews.setEnabled(false);
1784 expandViews.setText(MessageManager.getString("action.expand_views"));
1785 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1786 java.awt.event.KeyEvent.VK_X, 0, false));
1787 expandViews.addActionListener(new ActionListener()
1789 public void actionPerformed(ActionEvent e)
1791 expandViews_actionPerformed(e);
1794 pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
1795 pageSetup.addActionListener(new ActionListener()
1797 public void actionPerformed(ActionEvent e)
1799 pageSetup_actionPerformed(e);
1802 alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
1803 alignmentProperties.addActionListener(new ActionListener()
1805 public void actionPerformed(ActionEvent actionEvent)
1807 alignmentProperties();
1810 tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
1811 autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
1812 alignFrameMenuBar.add(fileMenu);
1813 alignFrameMenuBar.add(editMenu);
1814 alignFrameMenuBar.add(selectMenu);
1815 alignFrameMenuBar.add(viewMenu);
1816 alignFrameMenuBar.add(formatMenu);
1817 alignFrameMenuBar.add(colourMenu);
1818 alignFrameMenuBar.add(calculateMenu);
1819 alignFrameMenuBar.add(webService);
1820 fileMenu.add(fetchSequence);
1821 fileMenu.add(addSequenceMenu);
1822 fileMenu.add(reload);
1823 fileMenu.addSeparator();
1824 fileMenu.add(vamsasStore);
1826 fileMenu.add(saveAs);
1827 fileMenu.add(outputTextboxMenu);
1828 fileMenu.add(pageSetup);
1829 fileMenu.add(printMenuItem);
1830 fileMenu.addSeparator();
1831 fileMenu.add(jMenu2);
1832 fileMenu.add(exportFeatures);
1833 fileMenu.add(exportAnnotations);
1834 fileMenu.add(LoadtreeMenuItem);
1835 fileMenu.add(associatedData);
1836 fileMenu.addSeparator();
1837 fileMenu.add(closeMenuItem);
1838 editMenu.add(undoMenuItem);
1839 editMenu.add(redoMenuItem);
1842 editMenu.add(pasteMenu);
1843 editMenu.add(delete);
1844 editMenu.addSeparator();
1845 editMenu.add(remove2LeftMenuItem);
1846 editMenu.add(remove2RightMenuItem);
1847 editMenu.add(removeGappedColumnMenuItem);
1848 editMenu.add(removeAllGapsMenuItem);
1849 editMenu.add(removeRedundancyMenuItem);
1850 editMenu.addSeparator();
1851 // dont add these yet in the CVS build - they cannot be undone!
1852 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1853 // editMenu.add(justifyLeftMenuItem);
1854 // editMenu.add(justifyRightMenuItem);
1855 // editMenu.addSeparator();
1856 editMenu.add(padGapsMenuitem);
1857 viewMenu.add(newView);
1858 viewMenu.add(expandViews);
1859 viewMenu.add(gatherViews);
1860 viewMenu.addSeparator();
1861 viewMenu.add(jMenu3);
1862 viewMenu.add(hideMenu);
1863 viewMenu.addSeparator();
1864 viewMenu.add(followHighlightMenuItem);
1865 viewMenu.add(annotationPanelMenuItem);
1866 autoAnnMenu.add(applyAutoAnnotationSettings);
1867 autoAnnMenu.add(showConsensusHistogram);
1868 autoAnnMenu.add(showSequenceLogo);
1869 autoAnnMenu.add(normaliseSequenceLogo);
1870 autoAnnMenu.addSeparator();
1871 autoAnnMenu.add(showGroupConservation);
1872 autoAnnMenu.add(showGroupConsensus);
1873 viewMenu.add(autoAnnMenu);
1874 viewMenu.addSeparator();
1875 viewMenu.add(showSeqFeatures);
1876 // viewMenu.add(showSeqFeaturesHeight);
1878 viewMenu.add(openFeatureSettings);
1879 tooltipSettingsMenu.add(showDbRefsMenuitem);
1880 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1881 viewMenu.add(tooltipSettingsMenu);
1882 viewMenu.addSeparator();
1883 viewMenu.add(alignmentProperties);
1884 viewMenu.addSeparator();
1885 viewMenu.add(overviewMenuItem);
1886 colourMenu.add(applyToAllGroups);
1887 colourMenu.add(textColour);
1888 colourMenu.addSeparator();
1889 colourMenu.add(noColourmenuItem);
1890 colourMenu.add(clustalColour);
1891 colourMenu.add(BLOSUM62Colour);
1892 colourMenu.add(PIDColour);
1893 colourMenu.add(zappoColour);
1894 colourMenu.add(taylorColour);
1895 colourMenu.add(hydrophobicityColour);
1896 colourMenu.add(helixColour);
1897 colourMenu.add(strandColour);
1898 colourMenu.add(turnColour);
1899 colourMenu.add(buriedColour);
1900 colourMenu.add(nucleotideColour);
1901 colourMenu.add(purinePyrimidineColour);
1902 // colourMenu.add(covariationColour);
1903 colourMenu.add(tcoffeeColour);
1904 colourMenu.add(userDefinedColour);
1905 colourMenu.addSeparator();
1906 colourMenu.add(conservationMenuItem);
1907 colourMenu.add(modifyConservation);
1908 colourMenu.add(abovePIDThreshold);
1909 colourMenu.add(modifyPID);
1910 colourMenu.add(annotationColour);
1911 colourMenu.add(rnahelicesColour);
1912 calculateMenu.add(sort);
1913 calculateMenu.add(calculateTree);
1914 calculateMenu.addSeparator();
1915 calculateMenu.add(pairwiseAlignmentMenuItem);
1916 calculateMenu.add(PCAMenuItem);
1917 calculateMenu.addSeparator();
1918 calculateMenu.add(showTranslation);
1919 calculateMenu.add(showProducts);
1920 calculateMenu.add(autoCalculate);
1921 calculateMenu.add(sortByTree);
1922 calculateMenu.addSeparator();
1923 calculateMenu.add(extractScores);
1924 webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
1925 webService.add(webServiceNoServices);
1926 pasteMenu.add(pasteNew);
1927 pasteMenu.add(pasteThis);
1928 sort.add(sortIDMenuItem);
1929 sort.add(sortLengthMenuItem);
1930 sort.add(sortGroupMenuItem);
1931 sort.add(sortPairwiseMenuItem);
1932 sort.add(sortByTreeMenu);
1933 jMenu2.add(htmlMenuItem);
1934 jMenu2.add(epsFile);
1935 jMenu2.add(createPNG);
1936 addSequenceMenu.add(addFromFile);
1937 addSequenceMenu.add(addFromText);
1938 addSequenceMenu.add(addFromURL);
1939 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1940 statusPanel.add(statusBar, null);
1941 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1942 jMenu3.add(showAllColumns);
1943 jMenu3.add(showAllSeqs);
1944 jMenu3.add(showAllhidden);
1945 hideMenu.add(hideSelColumns);
1946 hideMenu.add(hideSelSequences);
1947 hideMenu.add(hideAllSelection);
1948 hideMenu.add(hideAllButSelection);
1950 formatMenu.add(font);
1951 formatMenu.addSeparator();
1952 formatMenu.add(wrapMenuItem);
1953 formatMenu.add(scaleAbove);
1954 formatMenu.add(scaleLeft);
1955 formatMenu.add(scaleRight);
1956 formatMenu.add(seqLimits);
1957 formatMenu.add(idRightAlign);
1958 formatMenu.add(hiddenMarkers);
1959 formatMenu.add(viewBoxesMenuItem);
1960 formatMenu.add(viewTextMenuItem);
1961 formatMenu.add(colourTextMenuItem);
1962 formatMenu.add(renderGapsMenuItem);
1963 formatMenu.add(centreColumnLabelsMenuItem);
1964 formatMenu.add(showNonconservedMenuItem);
1965 selectMenu.add(findMenuItem);
1966 selectMenu.addSeparator();
1967 selectMenu.add(selectAllSequenceMenuItem);
1968 selectMenu.add(deselectAllSequenceMenuItem);
1969 selectMenu.add(invertSequenceMenuItem);
1970 selectMenu.add(invertColSel);
1971 selectMenu.add(createGroup);
1972 selectMenu.add(unGroup);
1973 selectMenu.add(grpsFromSelection);
1974 selectMenu.add(deleteGroups);
1975 // TODO - determine if the listenToViewSelections button is needed : see bug
1977 // selectMenu.addSeparator();
1978 // selectMenu.add(listenToViewSelections);
1981 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1983 // TODO Auto-generated method stub
1987 protected void listenToViewSelections_actionPerformed(ActionEvent e)
1989 // TODO Auto-generated method stub
1993 protected void showAllhidden_actionPerformed(ActionEvent e)
1995 // TODO Auto-generated method stub
1999 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2001 // TODO Auto-generated method stub
2005 protected void hideAllSelection_actionPerformed(ActionEvent e)
2007 // TODO Auto-generated method stub
2011 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2013 // TODO Auto-generated method stub
2017 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2019 // TODO Auto-generated method stub
2023 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2025 // TODO Auto-generated method stub
2029 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2031 // TODO Auto-generated method stub
2035 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2037 // TODO Auto-generated method stub
2041 protected void showGroupConservation_actionPerformed(ActionEvent e)
2043 // TODO Auto-generated method stub
2047 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2049 // TODO Auto-generated method stub
2053 protected void showSeqFeaturesHeight_actionPerformed(
2054 ActionEvent actionEvent)
2056 // TODO Auto-generated method stub
2060 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2062 // TODO Auto-generated method stub
2066 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2068 // TODO Auto-generated method stub
2072 protected void followHighlight_actionPerformed()
2074 // TODO Auto-generated method stub
2078 protected void showNpFeats_actionPerformed(ActionEvent e)
2080 // TODO Auto-generated method stub
2084 protected void showDbRefs_actionPerformed(ActionEvent e)
2086 // TODO Auto-generated method stub
2090 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2094 protected void showProducts_actionPerformed(ActionEvent e)
2098 protected void buildSortByAnnotationScoresMenu()
2102 protected void extractScores_actionPerformed(ActionEvent e)
2106 protected void outputText_actionPerformed(ActionEvent e)
2110 public void addFromFile_actionPerformed(ActionEvent e)
2115 public void addFromText_actionPerformed(ActionEvent e)
2120 public void addFromURL_actionPerformed(ActionEvent e)
2125 public void exportFeatures_actionPerformed(ActionEvent e)
2130 public void exportAnnotations_actionPerformed(ActionEvent e)
2135 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2139 protected void closeMenuItem_actionPerformed(boolean b)
2143 protected void redoMenuItem_actionPerformed(ActionEvent e)
2147 protected void undoMenuItem_actionPerformed(ActionEvent e)
2151 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2155 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2159 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2163 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2167 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2171 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2175 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2179 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2183 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2187 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2191 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2195 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2199 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2203 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2207 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2211 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2215 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2219 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2223 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2227 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2231 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2235 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2239 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2243 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2247 protected void clustalColour_actionPerformed(ActionEvent e)
2251 protected void zappoColour_actionPerformed(ActionEvent e)
2255 protected void taylorColour_actionPerformed(ActionEvent e)
2259 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2263 protected void helixColour_actionPerformed(ActionEvent e)
2267 protected void strandColour_actionPerformed(ActionEvent e)
2271 protected void turnColour_actionPerformed(ActionEvent e)
2275 protected void buriedColour_actionPerformed(ActionEvent e)
2279 protected void userDefinedColour_actionPerformed(ActionEvent e)
2283 protected void PIDColour_actionPerformed(ActionEvent e)
2287 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2291 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2296 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2299 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2303 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2307 protected void printMenuItem_actionPerformed(ActionEvent e)
2311 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2315 protected void findMenuItem_actionPerformed(ActionEvent e)
2319 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2323 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2327 protected void nucleotideColour_actionPerformed(ActionEvent e)
2331 protected void deleteGroups_actionPerformed(ActionEvent e)
2335 protected void createGroup_actionPerformed(ActionEvent e)
2339 protected void unGroup_actionPerformed(ActionEvent e)
2343 protected void copy_actionPerformed(ActionEvent e)
2347 protected void cut_actionPerformed(ActionEvent e)
2351 protected void delete_actionPerformed(ActionEvent e)
2355 protected void pasteNew_actionPerformed(ActionEvent e)
2359 protected void pasteThis_actionPerformed(ActionEvent e)
2363 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2367 public void createPNG(java.io.File f)
2371 protected void font_actionPerformed(ActionEvent e)
2375 protected void seqLimit_actionPerformed(ActionEvent e)
2379 public void seqDBRef_actionPerformed(ActionEvent e)
2384 public void createEPS(java.io.File f)
2388 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2394 * Template method to handle the 'load T-Coffee scores' menu event.
2396 * Subclasses override this method to provide a custom action.
2401 protected void loadScores_actionPerformed(ActionEvent event)
2407 * Template method to handle the 'Color T-Coffee scores' menu event.
2409 * Subclasses override this method to provide a custom action.
2414 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2419 protected void jpred_actionPerformed(ActionEvent e)
2423 protected void scaleAbove_actionPerformed(ActionEvent e)
2427 protected void scaleLeft_actionPerformed(ActionEvent e)
2431 protected void scaleRight_actionPerformed(ActionEvent e)
2435 protected void modifyPID_actionPerformed(ActionEvent e)
2439 protected void modifyConservation_actionPerformed(ActionEvent e)
2443 protected void saveAs_actionPerformed(ActionEvent e)
2447 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2451 public void vamsasStore_actionPerformed(ActionEvent e)
2456 public void vamsasLoad_actionPerformed(ActionEvent e)
2461 public void showTranslation_actionPerformed(ActionEvent e)
2466 public void featureSettings_actionPerformed(ActionEvent e)
2471 public void fetchSequence_actionPerformed(ActionEvent e)
2476 public void smoothFont_actionPerformed(ActionEvent e)
2481 public void annotationColour_actionPerformed(ActionEvent e)
2486 public void rnahelicesColour_actionPerformed(ActionEvent e)
2491 public void associatedData_actionPerformed(ActionEvent e)
2496 public void autoCalculate_actionPerformed(ActionEvent e)
2501 public void sortByTreeOption_actionPerformed(ActionEvent e)
2506 public void showAllSeqs_actionPerformed(ActionEvent e)
2511 public void showAllColumns_actionPerformed(ActionEvent e)
2516 public void hideSelSequences_actionPerformed(ActionEvent e)
2521 public void hideSelColumns_actionPerformed(ActionEvent e)
2526 public void hiddenMarkers_actionPerformed(ActionEvent e)
2531 public void findPdbId_actionPerformed(ActionEvent e)
2536 public void enterPdbId_actionPerformed(ActionEvent e)
2541 public void pdbFile_actionPerformed(ActionEvent e)
2546 public void invertColSel_actionPerformed(ActionEvent e)
2551 public void tabSelectionChanged(int sel)
2556 public void tabbedPane_mousePressed(MouseEvent e)
2561 public void tabbedPane_focusGained(FocusEvent e)
2566 public void save_actionPerformed(ActionEvent e)
2571 public void reload_actionPerformed(ActionEvent e)
2576 public void newView_actionPerformed(ActionEvent e)
2581 public void textColour_actionPerformed(ActionEvent e)
2586 public void idRightAlign_actionPerformed(ActionEvent e)
2591 public void expandViews_actionPerformed(ActionEvent e)
2596 public void gatherViews_actionPerformed(ActionEvent e)
2601 public void buildTreeMenu()
2606 public void pageSetup_actionPerformed(ActionEvent e)
2611 public void alignmentProperties()