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 JMenuItem expandAlignment = new JMenuItem();
248 protected JMenu showProducts = new JMenu();
250 public JMenuItem openFeatureSettings = new JMenuItem();
252 JMenuItem fetchSequence = new JMenuItem();
254 JMenuItem annotationColour = new JMenuItem();
256 protected JMenuItem rnahelicesColour = new JMenuItem();
258 JMenuItem associatedData = new JMenuItem();
260 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
262 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
264 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
266 JMenu addSequenceMenu = new JMenu();
268 JMenuItem addFromFile = new JMenuItem();
270 JMenuItem addFromText = new JMenuItem();
272 JMenuItem addFromURL = new JMenuItem();
274 JMenuItem exportAnnotations = new JMenuItem();
276 JMenuItem exportFeatures = new JMenuItem();
278 protected JPanel statusPanel = new JPanel();
280 GridLayout gridLayout1 = new GridLayout();
282 JMenu jMenu3 = new JMenu();
284 JMenuItem showAllSeqs = new JMenuItem();
286 JMenuItem showAllColumns = new JMenuItem();
288 JMenu hideMenu = new JMenu();
290 JMenuItem hideSelSequences = new JMenuItem();
292 JMenuItem hideSelColumns = new JMenuItem();
294 JMenuItem hideAllButSelection = new JMenuItem();
296 JMenuItem hideAllSelection = new JMenuItem();
298 JMenuItem showAllhidden = new JMenuItem();
300 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
302 JMenuItem invertColSel = new JMenuItem();
304 protected JTabbedPane tabbedPane = new JTabbedPane();
306 JMenuItem save = new JMenuItem();
308 protected JMenuItem reload = new JMenuItem();
310 JMenuItem newView = new JMenuItem();
312 JMenuItem textColour = new JMenuItem();
314 JMenu formatMenu = new JMenu();
316 JMenu selectMenu = new JMenu();
318 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
320 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
322 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
324 protected JMenuItem gatherViews = new JMenuItem();
326 protected JMenuItem expandViews = new JMenuItem();
328 JMenuItem pageSetup = new JMenuItem();
330 JMenuItem alignmentProperties = new JMenuItem();
332 JMenu tooltipSettingsMenu = new JMenu();
334 private JMenuItem justifyLeftMenuItem = new JMenuItem();
336 private JMenuItem justifyRightMenuItem = new JMenuItem();
338 JMenu autoAnnMenu = new JMenu();
340 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
342 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
344 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
346 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
348 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
350 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
352 private JMenuItem grpsFromSelection = new JMenuItem();
359 setJMenuBar(alignFrameMenuBar);
361 // dynamically fill save as menu with available formats
362 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
364 JMenuItem item = new JMenuItem(
365 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
367 item.addActionListener(new java.awt.event.ActionListener()
369 public void actionPerformed(ActionEvent e)
371 outputText_actionPerformed(e);
375 outputTextboxMenu.add(item);
377 } catch (Exception e)
381 if (!new jalview.util.Platform().isAMac())
383 closeMenuItem.setMnemonic('C');
384 outputTextboxMenu.setMnemonic('T');
385 undoMenuItem.setMnemonic('Z');
386 redoMenuItem.setMnemonic('0');
387 copy.setMnemonic('C');
388 cut.setMnemonic('U');
389 pasteMenu.setMnemonic('P');
390 reload.setMnemonic('R');
393 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
395 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
396 .getUserColourSchemes().keys();
398 while (userColours.hasMoreElements())
400 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
401 userColours.nextElement().toString());
402 radioItem.setName("USER_DEFINED");
403 radioItem.addMouseListener(new MouseAdapter()
405 public void mousePressed(MouseEvent evt)
407 if (evt.isControlDown()
408 || SwingUtilities.isRightMouseButton(evt))
410 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
412 int option = JOptionPane.showInternalConfirmDialog(
413 jalview.gui.Desktop.desktop,
414 MessageManager.getString("label.remove_from_default_list"),
415 MessageManager.getString("label.remove_user_defined_colour"),
416 JOptionPane.YES_NO_OPTION);
417 if (option == JOptionPane.YES_OPTION)
419 jalview.gui.UserDefinedColours
420 .removeColourFromDefaults(radioItem.getText());
421 colourMenu.remove(radioItem);
425 radioItem.addActionListener(new ActionListener()
427 public void actionPerformed(ActionEvent evt)
429 userDefinedColour_actionPerformed(evt);
436 radioItem.addActionListener(new ActionListener()
438 public void actionPerformed(ActionEvent evt)
440 userDefinedColour_actionPerformed(evt);
443 colourMenu.insert(radioItem, 15);
444 colours.add(radioItem);
447 colours.add(noColourmenuItem);
448 colours.add(clustalColour);
449 colours.add(zappoColour);
450 colours.add(taylorColour);
451 colours.add(hydrophobicityColour);
452 colours.add(helixColour);
453 colours.add(strandColour);
454 colours.add(turnColour);
455 colours.add(buriedColour);
456 colours.add(userDefinedColour);
457 colours.add(PIDColour);
458 colours.add(BLOSUM62Colour);
459 colours.add(nucleotideColour);
460 colours.add(purinePyrimidineColour);
461 // colours.add(covariationColour);
462 colours.add(tcoffeeColour);
464 setColourSelected(jalview.bin.Cache
465 .getDefault("DEFAULT_COLOUR", "None"));
469 public void setColourSelected(String defaultColour)
472 if (defaultColour != null)
474 int index = ColourSchemeProperty
475 .getColourIndexFromName(defaultColour);
479 case ColourSchemeProperty.CLUSTAL:
480 clustalColour.setSelected(true);
484 case ColourSchemeProperty.BLOSUM:
485 BLOSUM62Colour.setSelected(true);
489 case ColourSchemeProperty.PID:
490 PIDColour.setSelected(true);
494 case ColourSchemeProperty.ZAPPO:
495 zappoColour.setSelected(true);
499 case ColourSchemeProperty.TAYLOR:
500 taylorColour.setSelected(true);
503 case ColourSchemeProperty.HYDROPHOBIC:
504 hydrophobicityColour.setSelected(true);
508 case ColourSchemeProperty.HELIX:
509 helixColour.setSelected(true);
513 case ColourSchemeProperty.STRAND:
514 strandColour.setSelected(true);
518 case ColourSchemeProperty.TURN:
519 turnColour.setSelected(true);
523 case ColourSchemeProperty.BURIED:
524 buriedColour.setSelected(true);
528 case ColourSchemeProperty.NUCLEOTIDE:
529 nucleotideColour.setSelected(true);
533 case ColourSchemeProperty.TCOFFEE:
534 tcoffeeColour.setSelected(true);
537 case ColourSchemeProperty.PURINEPYRIMIDINE:
538 purinePyrimidineColour.setSelected(true);
542 * case ColourSchemeProperty.COVARIATION:
543 * covariationColour.setSelected(true);
547 case ColourSchemeProperty.USER_DEFINED:
548 userDefinedColour.setSelected(true);
551 case ColourSchemeProperty.NONE:
553 noColourmenuItem.setSelected(true);
561 private void jbInit() throws Exception
563 fileMenu.setText(MessageManager.getString("action.file"));
564 saveAs.setText(MessageManager.getString("action.save_as") + "...");
565 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
566 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
567 .getMenuShortcutKeyMask()
568 | java.awt.event.KeyEvent.SHIFT_MASK, false));
569 saveAs.addActionListener(new ActionListener()
571 public void actionPerformed(ActionEvent e)
573 saveAs_actionPerformed(e);
576 closeMenuItem.setText(MessageManager.getString("action.close"));
577 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
578 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
579 .getMenuShortcutKeyMask(), false));
580 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
582 public void actionPerformed(ActionEvent e)
584 closeMenuItem_actionPerformed(false);
587 editMenu.setText(MessageManager.getString("action.edit"));
588 viewMenu.setText(MessageManager.getString("action.view"));
589 colourMenu.setText(MessageManager.getString("action.colour"));
590 calculateMenu.setText(MessageManager.getString("action.calculate"));
591 webService.setText(MessageManager.getString("action.web_service"));
592 selectAllSequenceMenuItem.setText(MessageManager.getString("action.select_all"));
593 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
594 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
595 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
596 selectAllSequenceMenuItem
597 .addActionListener(new java.awt.event.ActionListener()
599 public void actionPerformed(ActionEvent e)
601 selectAllSequenceMenuItem_actionPerformed(e);
604 deselectAllSequenceMenuItem.setText(MessageManager.getString("action.deselect_all"));
605 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
606 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
607 deselectAllSequenceMenuItem
608 .addActionListener(new java.awt.event.ActionListener()
610 public void actionPerformed(ActionEvent e)
612 deselectAllSequenceMenuItem_actionPerformed(e);
615 invertSequenceMenuItem.setText(MessageManager.getString("action.invert_sequence_selection"));
616 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
617 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
618 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
619 invertSequenceMenuItem
620 .addActionListener(new java.awt.event.ActionListener()
622 public void actionPerformed(ActionEvent e)
624 invertSequenceMenuItem_actionPerformed(e);
627 grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
628 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
630 public void actionPerformed(ActionEvent e)
632 makeGrpsFromSelection_actionPerformed(e);
635 expandAlignment.setText(MessageManager.getString("action.view_flanking_regions"));
636 expandAlignment.addActionListener(new java.awt.event.ActionListener() {
638 public void actionPerformed(ActionEvent e)
643 remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
644 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
645 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
646 .getMenuShortcutKeyMask(), false));
648 .addActionListener(new java.awt.event.ActionListener()
650 public void actionPerformed(ActionEvent e)
652 remove2LeftMenuItem_actionPerformed(e);
655 remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
656 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
657 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
658 .getMenuShortcutKeyMask(), false));
660 .addActionListener(new java.awt.event.ActionListener()
662 public void actionPerformed(ActionEvent e)
664 remove2RightMenuItem_actionPerformed(e);
667 removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
668 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
669 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
670 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
671 removeGappedColumnMenuItem
672 .addActionListener(new java.awt.event.ActionListener()
674 public void actionPerformed(ActionEvent e)
676 removeGappedColumnMenuItem_actionPerformed(e);
679 removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
680 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
681 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
682 .getDefaultToolkit().getMenuShortcutKeyMask()
683 | java.awt.event.KeyEvent.SHIFT_MASK, false));
684 removeAllGapsMenuItem
685 .addActionListener(new java.awt.event.ActionListener()
687 public void actionPerformed(ActionEvent e)
689 removeAllGapsMenuItem_actionPerformed(e);
692 justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
694 .addActionListener(new java.awt.event.ActionListener()
696 public void actionPerformed(ActionEvent e)
698 justifyLeftMenuItem_actionPerformed(e);
701 justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
703 .addActionListener(new java.awt.event.ActionListener()
705 public void actionPerformed(ActionEvent e)
707 justifyRightMenuItem_actionPerformed(e);
710 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
711 viewBoxesMenuItem.setState(true);
712 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
714 public void actionPerformed(ActionEvent e)
716 viewBoxesMenuItem_actionPerformed(e);
719 viewTextMenuItem.setText(MessageManager.getString("action.text"));
720 viewTextMenuItem.setState(true);
721 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
723 public void actionPerformed(ActionEvent e)
725 viewTextMenuItem_actionPerformed(e);
728 showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
729 showNonconservedMenuItem.setState(false);
730 showNonconservedMenuItem
731 .addActionListener(new java.awt.event.ActionListener()
733 public void actionPerformed(ActionEvent e)
735 showUnconservedMenuItem_actionPerformed(e);
738 sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
740 .addActionListener(new java.awt.event.ActionListener()
742 public void actionPerformed(ActionEvent e)
744 sortPairwiseMenuItem_actionPerformed(e);
747 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
748 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
750 public void actionPerformed(ActionEvent e)
752 sortIDMenuItem_actionPerformed(e);
755 sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
757 .addActionListener(new java.awt.event.ActionListener()
759 public void actionPerformed(ActionEvent e)
761 sortLengthMenuItem_actionPerformed(e);
764 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
765 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
767 public void actionPerformed(ActionEvent e)
769 sortGroupMenuItem_actionPerformed(e);
772 removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
773 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
774 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
775 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
776 removeRedundancyMenuItem
777 .addActionListener(new java.awt.event.ActionListener()
779 public void actionPerformed(ActionEvent e)
781 removeRedundancyMenuItem_actionPerformed(e);
784 pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
785 pairwiseAlignmentMenuItem
786 .addActionListener(new java.awt.event.ActionListener()
788 public void actionPerformed(ActionEvent e)
790 pairwiseAlignmentMenuItem_actionPerformed(e);
793 PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
794 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
796 public void actionPerformed(ActionEvent e)
798 PCAMenuItem_actionPerformed(e);
801 averageDistanceTreeMenuItem
802 .setText(MessageManager.getString("label.average_distance_identity"));
803 averageDistanceTreeMenuItem
804 .addActionListener(new java.awt.event.ActionListener()
806 public void actionPerformed(ActionEvent e)
808 averageDistanceTreeMenuItem_actionPerformed(e);
811 neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
812 neighbourTreeMenuItem
813 .addActionListener(new java.awt.event.ActionListener()
815 public void actionPerformed(ActionEvent e)
817 neighbourTreeMenuItem_actionPerformed(e);
820 this.getContentPane().setLayout(borderLayout1);
821 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
822 statusBar.setBackground(Color.white);
823 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
824 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
825 statusBar.setText(MessageManager.getString("label.status_bar"));
826 outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
827 clustalColour.setText(MessageManager.getString("label.clustalx"));
829 clustalColour.addActionListener(new java.awt.event.ActionListener()
831 public void actionPerformed(ActionEvent e)
833 clustalColour_actionPerformed(e);
836 zappoColour.setText(MessageManager.getString("label.zappo"));
837 zappoColour.addActionListener(new java.awt.event.ActionListener()
839 public void actionPerformed(ActionEvent e)
841 zappoColour_actionPerformed(e);
844 taylorColour.setText(MessageManager.getString("label.taylor"));
845 taylorColour.addActionListener(new java.awt.event.ActionListener()
847 public void actionPerformed(ActionEvent e)
849 taylorColour_actionPerformed(e);
852 hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
854 .addActionListener(new java.awt.event.ActionListener()
856 public void actionPerformed(ActionEvent e)
858 hydrophobicityColour_actionPerformed(e);
861 helixColour.setText(MessageManager.getString("label.helix_propensity"));
862 helixColour.addActionListener(new java.awt.event.ActionListener()
864 public void actionPerformed(ActionEvent e)
866 helixColour_actionPerformed(e);
869 strandColour.setText(MessageManager.getString("label.strand_propensity"));
870 strandColour.addActionListener(new java.awt.event.ActionListener()
872 public void actionPerformed(ActionEvent e)
874 strandColour_actionPerformed(e);
877 turnColour.setText(MessageManager.getString("Turn Propensity"));
878 turnColour.addActionListener(new java.awt.event.ActionListener()
880 public void actionPerformed(ActionEvent e)
882 turnColour_actionPerformed(e);
885 buriedColour.setText(MessageManager.getString("Buried Index"));
886 buriedColour.addActionListener(new java.awt.event.ActionListener()
888 public void actionPerformed(ActionEvent e)
890 buriedColour_actionPerformed(e);
893 userDefinedColour.setText(MessageManager.getString("action.user_defined"));
894 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
896 public void actionPerformed(ActionEvent e)
898 userDefinedColour_actionPerformed(e);
901 PIDColour.setText(MessageManager.getString("label.percentage_identity"));
902 PIDColour.addActionListener(new java.awt.event.ActionListener()
904 public void actionPerformed(ActionEvent e)
906 PIDColour_actionPerformed(e);
909 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
910 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
912 public void actionPerformed(ActionEvent e)
914 BLOSUM62Colour_actionPerformed(e);
917 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
918 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
920 public void actionPerformed(ActionEvent e)
922 nucleotideColour_actionPerformed(e);
926 purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
927 purinePyrimidineColour
928 .addActionListener(new java.awt.event.ActionListener()
930 public void actionPerformed(ActionEvent e)
932 purinePyrimidineColour_actionPerformed(e);
936 * covariationColour.setText("Covariation");
937 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
938 * public void actionPerformed(ActionEvent e) {
939 * covariationColour_actionPerformed(e); } });
942 avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
943 avDistanceTreeBlosumMenuItem
944 .addActionListener(new java.awt.event.ActionListener()
946 public void actionPerformed(ActionEvent e)
948 avTreeBlosumMenuItem_actionPerformed(e);
951 njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
953 .addActionListener(new java.awt.event.ActionListener()
955 public void actionPerformed(ActionEvent e)
957 njTreeBlosumMenuItem_actionPerformed(e);
960 annotationPanelMenuItem.setActionCommand("");
961 annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
962 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
963 "SHOW_ANNOTATIONS", true));
964 annotationPanelMenuItem
965 .addActionListener(new java.awt.event.ActionListener()
967 public void actionPerformed(ActionEvent e)
969 annotationPanelMenuItem_actionPerformed(e);
972 colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
974 .addActionListener(new java.awt.event.ActionListener()
976 public void actionPerformed(ActionEvent e)
978 colourTextMenuItem_actionPerformed(e);
981 htmlMenuItem.setText(MessageManager.getString("label.html"));
982 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
984 public void actionPerformed(ActionEvent e)
986 htmlMenuItem_actionPerformed(e);
989 overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
990 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
992 public void actionPerformed(ActionEvent e)
994 overviewMenuItem_actionPerformed(e);
997 undoMenuItem.setEnabled(false);
998 undoMenuItem.setText(MessageManager.getString("action.undo"));
999 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1000 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1001 .getMenuShortcutKeyMask(), false));
1002 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1004 public void actionPerformed(ActionEvent e)
1006 undoMenuItem_actionPerformed(e);
1009 redoMenuItem.setEnabled(false);
1010 redoMenuItem.setText(MessageManager.getString("action.redo"));
1011 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1012 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1013 .getMenuShortcutKeyMask(), false));
1014 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1016 public void actionPerformed(ActionEvent e)
1018 redoMenuItem_actionPerformed(e);
1021 conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
1022 conservationMenuItem
1023 .addActionListener(new java.awt.event.ActionListener()
1025 public void actionPerformed(ActionEvent e)
1027 conservationMenuItem_actionPerformed(e);
1030 noColourmenuItem.setText(MessageManager.getString("label.none"));
1031 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1033 public void actionPerformed(ActionEvent e)
1035 noColourmenuItem_actionPerformed(e);
1038 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1039 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1041 public void actionPerformed(ActionEvent e)
1043 wrapMenuItem_actionPerformed(e);
1046 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1047 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1048 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1049 .getMenuShortcutKeyMask(), false));
1050 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1052 public void actionPerformed(ActionEvent e)
1054 printMenuItem_actionPerformed(e);
1057 renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
1058 renderGapsMenuItem.setState(true);
1060 .addActionListener(new java.awt.event.ActionListener()
1062 public void actionPerformed(ActionEvent e)
1064 renderGapsMenuItem_actionPerformed(e);
1067 findMenuItem.setText(MessageManager.getString("action.find"));
1068 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1069 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1070 .getMenuShortcutKeyMask(), false));
1071 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1073 public void actionPerformed(ActionEvent e)
1075 findMenuItem_actionPerformed(e);
1078 abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
1079 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1081 public void actionPerformed(ActionEvent e)
1083 abovePIDThreshold_actionPerformed(e);
1086 showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
1087 showSeqFeatures.addActionListener(new ActionListener()
1089 public void actionPerformed(ActionEvent actionEvent)
1091 showSeqFeatures_actionPerformed(actionEvent);
1095 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1096 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1097 * void actionPerformed(ActionEvent actionEvent) {
1098 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1100 showDbRefsMenuitem.setText(MessageManager.getString("label.show_database_refs"));
1101 showDbRefsMenuitem.addActionListener(new ActionListener()
1104 public void actionPerformed(ActionEvent e)
1106 showDbRefs_actionPerformed(e);
1110 showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
1111 showNpFeatsMenuitem.addActionListener(new ActionListener()
1114 public void actionPerformed(ActionEvent e)
1116 showNpFeats_actionPerformed(e);
1120 showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
1121 showGroupConservation.addActionListener(new ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 showGroupConservation_actionPerformed(e);
1131 showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
1132 showGroupConsensus.addActionListener(new ActionListener()
1135 public void actionPerformed(ActionEvent e)
1137 showGroupConsensus_actionPerformed(e);
1141 showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
1142 showConsensusHistogram.addActionListener(new ActionListener()
1145 public void actionPerformed(ActionEvent e)
1147 showConsensusHistogram_actionPerformed(e);
1151 showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
1152 showSequenceLogo.addActionListener(new ActionListener()
1155 public void actionPerformed(ActionEvent e)
1157 showSequenceLogo_actionPerformed(e);
1161 normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
1162 normaliseSequenceLogo.addActionListener(new ActionListener()
1165 public void actionPerformed(ActionEvent e)
1167 normaliseSequenceLogo_actionPerformed(e);
1171 applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
1172 applyAutoAnnotationSettings.setState(false);
1173 applyAutoAnnotationSettings.setVisible(true);
1174 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1177 public void actionPerformed(ActionEvent e)
1179 applyAutoAnnotationSettings_actionPerformed(e);
1184 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1185 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1187 public void actionPerformed(ActionEvent e)
1189 nucleotideColour_actionPerformed(e);
1193 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1194 tcoffeeColour.setEnabled(false);
1195 tcoffeeColour.addActionListener(new ActionListener()
1199 public void actionPerformed(ActionEvent e)
1201 tcoffeeColorScheme_actionPerformed(e);
1205 deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
1206 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1207 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1208 .getMenuShortcutKeyMask(), false));
1209 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1211 public void actionPerformed(ActionEvent e)
1213 deleteGroups_actionPerformed(e);
1216 createGroup.setText(MessageManager.getString("action.create_groups"));
1217 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1218 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1219 .getMenuShortcutKeyMask(), false));
1220 createGroup.addActionListener(new java.awt.event.ActionListener()
1222 public void actionPerformed(ActionEvent e)
1224 createGroup_actionPerformed(e);
1227 unGroup.setText(MessageManager.getString("action.remove_group"));
1228 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1229 java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
1230 .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
1231 unGroup.addActionListener(new java.awt.event.ActionListener()
1233 public void actionPerformed(ActionEvent e)
1235 unGroup_actionPerformed(e);
1238 copy.setText(MessageManager.getString("action.copy"));
1239 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1240 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1241 .getMenuShortcutKeyMask(), false));
1243 copy.addActionListener(new java.awt.event.ActionListener()
1245 public void actionPerformed(ActionEvent e)
1247 copy_actionPerformed(e);
1250 cut.setText(MessageManager.getString("action.cut"));
1251 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1252 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1253 .getMenuShortcutKeyMask(), false));
1254 cut.addActionListener(new java.awt.event.ActionListener()
1256 public void actionPerformed(ActionEvent e)
1258 cut_actionPerformed(e);
1261 delete.setText(MessageManager.getString("action.delete"));
1262 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1263 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1264 delete.addActionListener(new java.awt.event.ActionListener()
1266 public void actionPerformed(ActionEvent e)
1268 delete_actionPerformed(e);
1271 pasteMenu.setText(MessageManager.getString("action.paste"));
1272 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1273 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1274 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1275 .getMenuShortcutKeyMask()
1276 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1277 pasteNew.addActionListener(new java.awt.event.ActionListener()
1279 public void actionPerformed(ActionEvent e)
1281 pasteNew_actionPerformed(e);
1284 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1285 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1286 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1287 .getMenuShortcutKeyMask(), false));
1288 pasteThis.addActionListener(new java.awt.event.ActionListener()
1290 public void actionPerformed(ActionEvent e)
1292 pasteThis_actionPerformed(e);
1295 applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
1296 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1298 public void actionPerformed(ActionEvent e)
1300 applyToAllGroups_actionPerformed(e);
1303 createPNG.addActionListener(new java.awt.event.ActionListener()
1305 public void actionPerformed(ActionEvent e)
1310 createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
1311 createPNG.setText("PNG");
1312 font.setText(MessageManager.getString("action.font"));
1313 font.addActionListener(new java.awt.event.ActionListener()
1315 public void actionPerformed(ActionEvent e)
1317 font_actionPerformed(e);
1321 seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
1322 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1323 seqLimits.addActionListener(new java.awt.event.ActionListener()
1325 public void actionPerformed(ActionEvent e)
1327 seqLimit_actionPerformed(e);
1330 epsFile.setText("EPS");
1331 epsFile.addActionListener(new java.awt.event.ActionListener()
1333 public void actionPerformed(ActionEvent e)
1338 LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
1339 LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree"));
1340 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1342 public void actionPerformed(ActionEvent e)
1344 LoadtreeMenuItem_actionPerformed(e);
1348 scaleAbove.setVisible(false);
1349 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1350 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1352 public void actionPerformed(ActionEvent e)
1354 scaleAbove_actionPerformed(e);
1357 scaleLeft.setVisible(false);
1358 scaleLeft.setSelected(true);
1359 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1360 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1362 public void actionPerformed(ActionEvent e)
1364 scaleLeft_actionPerformed(e);
1367 scaleRight.setVisible(false);
1368 scaleRight.setSelected(true);
1369 scaleRight.setText(MessageManager.getString("action.scale_right"));
1370 scaleRight.addActionListener(new java.awt.event.ActionListener()
1372 public void actionPerformed(ActionEvent e)
1374 scaleRight_actionPerformed(e);
1377 centreColumnLabelsMenuItem.setVisible(true);
1378 centreColumnLabelsMenuItem.setState(false);
1379 centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
1380 centreColumnLabelsMenuItem
1381 .addActionListener(new java.awt.event.ActionListener()
1383 public void actionPerformed(ActionEvent e)
1385 centreColumnLabels_actionPerformed(e);
1388 followHighlightMenuItem.setVisible(true);
1389 followHighlightMenuItem.setState(true);
1390 followHighlightMenuItem.setText(MessageManager.getString("label.automatic_scrolling"));
1391 followHighlightMenuItem.addActionListener(new ActionListener()
1394 public void actionPerformed(ActionEvent e)
1396 followHighlight_actionPerformed();
1401 modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
1402 modifyPID.addActionListener(new java.awt.event.ActionListener()
1404 public void actionPerformed(ActionEvent e)
1406 modifyPID_actionPerformed(e);
1409 modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
1411 .addActionListener(new java.awt.event.ActionListener()
1413 public void actionPerformed(ActionEvent e)
1415 modifyConservation_actionPerformed(e);
1418 sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order"));
1419 sort.setText(MessageManager.getString("action.sort"));
1420 sort.addMenuListener(new MenuListener()
1422 public void menuSelected(MenuEvent e)
1427 public void menuDeselected(MenuEvent e)
1431 public void menuCanceled(MenuEvent e)
1435 sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
1436 sort.add(sortByAnnotScore);
1437 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1440 public void menuCanceled(MenuEvent e)
1444 public void menuDeselected(MenuEvent e)
1448 public void menuSelected(MenuEvent e)
1450 buildSortByAnnotationScoresMenu();
1453 sortByAnnotScore.setVisible(false);
1455 calculateTree.setText(MessageManager.getString("action.calculate_tree"));
1457 jMenu2.setText(MessageManager.getString("label.export_image"));
1458 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1459 padGapsMenuitem.setState(jalview.bin.Cache
1460 .getDefault("PAD_GAPS", false));
1461 padGapsMenuitem.addActionListener(new ActionListener()
1463 public void actionPerformed(ActionEvent e)
1465 padGapsMenuitem_actionPerformed(e);
1468 vamsasStore.setVisible(false);
1469 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1470 vamsasStore.addActionListener(new ActionListener()
1472 public void actionPerformed(ActionEvent e)
1474 vamsasStore_actionPerformed(e);
1477 showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
1478 showTranslation.addActionListener(new ActionListener()
1480 public void actionPerformed(ActionEvent e)
1482 showTranslation_actionPerformed(e);
1485 extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
1486 extractScores.addActionListener(new ActionListener()
1488 public void actionPerformed(ActionEvent e)
1490 extractScores_actionPerformed(e);
1493 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1495 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1497 * showProducts.addActionListener(new ActionListener() {
1499 * public void actionPerformed(ActionEvent e) {
1500 * showProducts_actionPerformed(e); } });
1502 openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
1503 openFeatureSettings.addActionListener(new ActionListener()
1505 public void actionPerformed(ActionEvent e)
1507 featureSettings_actionPerformed(e);
1510 fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
1511 fetchSequence.addActionListener(new ActionListener()
1513 public void actionPerformed(ActionEvent e)
1515 fetchSequence_actionPerformed(e);
1519 annotationColour.setText(MessageManager.getString("action.by_annotation"));
1520 annotationColour.addActionListener(new ActionListener()
1522 public void actionPerformed(ActionEvent e)
1524 annotationColour_actionPerformed(e);
1528 rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
1529 rnahelicesColour.addActionListener(new ActionListener()
1531 public void actionPerformed(ActionEvent e)
1533 rnahelicesColour_actionPerformed(e);
1537 associatedData.setText(MessageManager.getString("label.load_features_annotations"));
1538 associatedData.addActionListener(new ActionListener()
1540 public void actionPerformed(ActionEvent e)
1542 associatedData_actionPerformed(e);
1545 autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
1546 autoCalculate.setState(jalview.bin.Cache.getDefault(
1547 "AUTO_CALC_CONSENSUS", true));
1548 autoCalculate.addActionListener(new ActionListener()
1550 public void actionPerformed(ActionEvent e)
1552 autoCalculate_actionPerformed(e);
1555 sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
1557 .setToolTipText("<html>" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1559 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1560 sortByTree.addActionListener(new ActionListener()
1562 public void actionPerformed(ActionEvent e)
1564 sortByTreeOption_actionPerformed(e);
1568 listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
1569 listenToViewSelections
1570 .setToolTipText("<html>" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1571 listenToViewSelections.setState(false);
1572 listenToViewSelections.addActionListener(new ActionListener()
1574 public void actionPerformed(ActionEvent e)
1576 listenToViewSelections_actionPerformed(e);
1580 addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
1581 addFromFile.setText(MessageManager.getString("label.from_file"));
1582 addFromFile.addActionListener(new ActionListener()
1584 public void actionPerformed(ActionEvent e)
1586 addFromFile_actionPerformed(e);
1589 addFromText.setText(MessageManager.getString("label.from_textbox"));
1590 addFromText.addActionListener(new ActionListener()
1592 public void actionPerformed(ActionEvent e)
1594 addFromText_actionPerformed(e);
1597 addFromURL.setText(MessageManager.getString("label.from_url"));
1598 addFromURL.addActionListener(new ActionListener()
1600 public void actionPerformed(ActionEvent e)
1602 addFromURL_actionPerformed(e);
1605 exportFeatures.setText(MessageManager.getString("label.export_features"));
1606 exportFeatures.addActionListener(new ActionListener()
1608 public void actionPerformed(ActionEvent e)
1610 exportFeatures_actionPerformed(e);
1613 exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
1614 exportAnnotations.addActionListener(new ActionListener()
1616 public void actionPerformed(ActionEvent e)
1618 exportAnnotations_actionPerformed(e);
1621 statusPanel.setLayout(gridLayout1);
1622 jMenu3.setText(MessageManager.getString("action.show"));
1623 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1624 showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1625 showAllSeqs.addActionListener(new ActionListener()
1627 public void actionPerformed(ActionEvent e)
1629 showAllSeqs_actionPerformed(e);
1632 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1633 showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1634 showAllColumns.addActionListener(new ActionListener()
1636 public void actionPerformed(ActionEvent e)
1638 showAllColumns_actionPerformed(e);
1641 hideMenu.setText(MessageManager.getString("action.hide"));
1642 hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
1643 hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1644 hideSelSequences.addActionListener(new ActionListener()
1646 public void actionPerformed(ActionEvent e)
1648 hideSelSequences_actionPerformed(e);
1651 hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
1652 hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1653 hideSelColumns.addActionListener(new ActionListener()
1655 public void actionPerformed(ActionEvent e)
1657 hideSelColumns_actionPerformed(e);
1660 hideAllSelection.setText(MessageManager.getString("label.selected_region"));
1661 hideAllSelection.addActionListener(new ActionListener()
1663 public void actionPerformed(ActionEvent e)
1665 hideAllSelection_actionPerformed(e);
1668 // TODO: should be hidden if no selection exists.
1669 hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
1670 hideAllButSelection.addActionListener(new ActionListener()
1672 public void actionPerformed(ActionEvent e)
1674 hideAllButSelection_actionPerformed(e);
1677 showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
1679 .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
1680 showAllhidden.addActionListener(new ActionListener()
1682 public void actionPerformed(ActionEvent e)
1684 showAllhidden_actionPerformed(e);
1688 hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
1689 hiddenMarkers.addActionListener(new ActionListener()
1691 public void actionPerformed(ActionEvent e)
1693 hiddenMarkers_actionPerformed(e);
1696 invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
1697 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1698 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1699 .getMenuShortcutKeyMask()
1700 | java.awt.event.KeyEvent.ALT_MASK, false));
1701 invertColSel.addActionListener(new ActionListener()
1703 public void actionPerformed(ActionEvent e)
1705 invertColSel_actionPerformed(e);
1708 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1710 public void stateChanged(ChangeEvent evt)
1712 JTabbedPane pane = (JTabbedPane) evt.getSource();
1713 int sel = pane.getSelectedIndex();
1714 tabSelectionChanged(sel);
1717 tabbedPane.addMouseListener(new MouseAdapter()
1719 public void mousePressed(MouseEvent e)
1721 tabbedPane_mousePressed(e);
1724 tabbedPane.addFocusListener(new FocusAdapter()
1726 public void focusGained(FocusEvent e)
1728 tabbedPane_focusGained(e);
1731 save.setText(MessageManager.getString("action.save"));
1732 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1733 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1734 .getMenuShortcutKeyMask(), false));
1735 save.addActionListener(new ActionListener()
1737 public void actionPerformed(ActionEvent e)
1739 save_actionPerformed(e);
1742 reload.setEnabled(false);
1743 reload.setText(MessageManager.getString("action.reload"));
1744 reload.addActionListener(new ActionListener()
1746 public void actionPerformed(ActionEvent e)
1748 reload_actionPerformed(e);
1751 newView.setText(MessageManager.getString("action.new_view"));
1752 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1753 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1754 .getMenuShortcutKeyMask(), false));
1755 newView.addActionListener(new ActionListener()
1757 public void actionPerformed(ActionEvent e)
1759 newView_actionPerformed(e);
1762 tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
1763 textColour.setText(MessageManager.getString("label.colour_text") + "...");
1764 textColour.addActionListener(new ActionListener()
1766 public void actionPerformed(ActionEvent e)
1768 textColour_actionPerformed(e);
1771 formatMenu.setText(MessageManager.getString("action.format"));
1772 selectMenu.setText(MessageManager.getString("action.select"));
1773 idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id"));
1774 idRightAlign.addActionListener(new ActionListener()
1776 public void actionPerformed(ActionEvent e)
1778 idRightAlign_actionPerformed(e);
1781 gatherViews.setEnabled(false);
1782 gatherViews.setText(MessageManager.getString("action.gather_views"));
1783 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1784 java.awt.event.KeyEvent.VK_G, 0, false));
1785 gatherViews.addActionListener(new ActionListener()
1787 public void actionPerformed(ActionEvent e)
1789 gatherViews_actionPerformed(e);
1792 expandViews.setEnabled(false);
1793 expandViews.setText(MessageManager.getString("action.expand_views"));
1794 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1795 java.awt.event.KeyEvent.VK_X, 0, false));
1796 expandViews.addActionListener(new ActionListener()
1798 public void actionPerformed(ActionEvent e)
1800 expandViews_actionPerformed(e);
1803 pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
1804 pageSetup.addActionListener(new ActionListener()
1806 public void actionPerformed(ActionEvent e)
1808 pageSetup_actionPerformed(e);
1811 alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
1812 alignmentProperties.addActionListener(new ActionListener()
1814 public void actionPerformed(ActionEvent actionEvent)
1816 alignmentProperties();
1819 tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
1820 autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
1821 alignFrameMenuBar.add(fileMenu);
1822 alignFrameMenuBar.add(editMenu);
1823 alignFrameMenuBar.add(selectMenu);
1824 alignFrameMenuBar.add(viewMenu);
1825 alignFrameMenuBar.add(formatMenu);
1826 alignFrameMenuBar.add(colourMenu);
1827 alignFrameMenuBar.add(calculateMenu);
1828 alignFrameMenuBar.add(webService);
1829 fileMenu.add(fetchSequence);
1830 fileMenu.add(addSequenceMenu);
1831 fileMenu.add(reload);
1832 fileMenu.addSeparator();
1833 fileMenu.add(vamsasStore);
1835 fileMenu.add(saveAs);
1836 fileMenu.add(outputTextboxMenu);
1837 fileMenu.add(pageSetup);
1838 fileMenu.add(printMenuItem);
1839 fileMenu.addSeparator();
1840 fileMenu.add(jMenu2);
1841 fileMenu.add(exportFeatures);
1842 fileMenu.add(exportAnnotations);
1843 fileMenu.add(LoadtreeMenuItem);
1844 fileMenu.add(associatedData);
1845 fileMenu.addSeparator();
1846 fileMenu.add(closeMenuItem);
1847 editMenu.add(undoMenuItem);
1848 editMenu.add(redoMenuItem);
1851 editMenu.add(pasteMenu);
1852 editMenu.add(delete);
1853 editMenu.addSeparator();
1854 editMenu.add(remove2LeftMenuItem);
1855 editMenu.add(remove2RightMenuItem);
1856 editMenu.add(removeGappedColumnMenuItem);
1857 editMenu.add(removeAllGapsMenuItem);
1858 editMenu.add(removeRedundancyMenuItem);
1859 editMenu.addSeparator();
1860 // dont add these yet in the CVS build - they cannot be undone!
1861 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1862 // editMenu.add(justifyLeftMenuItem);
1863 // editMenu.add(justifyRightMenuItem);
1864 // editMenu.addSeparator();
1865 editMenu.add(padGapsMenuitem);
1866 viewMenu.add(newView);
1867 viewMenu.add(expandViews);
1868 viewMenu.add(gatherViews);
1869 viewMenu.addSeparator();
1870 viewMenu.add(jMenu3);
1871 viewMenu.add(hideMenu);
1872 viewMenu.addSeparator();
1873 viewMenu.add(followHighlightMenuItem);
1874 viewMenu.add(annotationPanelMenuItem);
1875 autoAnnMenu.add(applyAutoAnnotationSettings);
1876 autoAnnMenu.add(showConsensusHistogram);
1877 autoAnnMenu.add(showSequenceLogo);
1878 autoAnnMenu.add(normaliseSequenceLogo);
1879 autoAnnMenu.addSeparator();
1880 autoAnnMenu.add(showGroupConservation);
1881 autoAnnMenu.add(showGroupConsensus);
1882 viewMenu.add(autoAnnMenu);
1883 viewMenu.addSeparator();
1884 viewMenu.add(showSeqFeatures);
1885 // viewMenu.add(showSeqFeaturesHeight);
1887 viewMenu.add(openFeatureSettings);
1888 tooltipSettingsMenu.add(showDbRefsMenuitem);
1889 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1890 viewMenu.add(tooltipSettingsMenu);
1891 viewMenu.addSeparator();
1892 viewMenu.add(alignmentProperties);
1893 viewMenu.addSeparator();
1894 viewMenu.add(overviewMenuItem);
1895 colourMenu.add(applyToAllGroups);
1896 colourMenu.add(textColour);
1897 colourMenu.addSeparator();
1898 colourMenu.add(noColourmenuItem);
1899 colourMenu.add(clustalColour);
1900 colourMenu.add(BLOSUM62Colour);
1901 colourMenu.add(PIDColour);
1902 colourMenu.add(zappoColour);
1903 colourMenu.add(taylorColour);
1904 colourMenu.add(hydrophobicityColour);
1905 colourMenu.add(helixColour);
1906 colourMenu.add(strandColour);
1907 colourMenu.add(turnColour);
1908 colourMenu.add(buriedColour);
1909 colourMenu.add(nucleotideColour);
1910 colourMenu.add(purinePyrimidineColour);
1911 // colourMenu.add(covariationColour);
1912 colourMenu.add(tcoffeeColour);
1913 colourMenu.add(userDefinedColour);
1914 colourMenu.addSeparator();
1915 colourMenu.add(conservationMenuItem);
1916 colourMenu.add(modifyConservation);
1917 colourMenu.add(abovePIDThreshold);
1918 colourMenu.add(modifyPID);
1919 colourMenu.add(annotationColour);
1920 colourMenu.add(rnahelicesColour);
1921 calculateMenu.add(sort);
1922 calculateMenu.add(calculateTree);
1923 calculateMenu.addSeparator();
1924 calculateMenu.add(pairwiseAlignmentMenuItem);
1925 calculateMenu.add(PCAMenuItem);
1926 calculateMenu.addSeparator();
1927 calculateMenu.add(showTranslation);
1928 calculateMenu.add(showProducts);
1929 calculateMenu.add(autoCalculate);
1930 calculateMenu.add(sortByTree);
1931 calculateMenu.addSeparator();
1932 calculateMenu.add(extractScores);
1933 webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
1934 webService.add(webServiceNoServices);
1935 pasteMenu.add(pasteNew);
1936 pasteMenu.add(pasteThis);
1937 sort.add(sortIDMenuItem);
1938 sort.add(sortLengthMenuItem);
1939 sort.add(sortGroupMenuItem);
1940 sort.add(sortPairwiseMenuItem);
1941 sort.add(sortByTreeMenu);
1942 jMenu2.add(htmlMenuItem);
1943 jMenu2.add(epsFile);
1944 jMenu2.add(createPNG);
1945 addSequenceMenu.add(addFromFile);
1946 addSequenceMenu.add(addFromText);
1947 addSequenceMenu.add(addFromURL);
1948 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1949 statusPanel.add(statusBar, null);
1950 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1951 jMenu3.add(showAllColumns);
1952 jMenu3.add(showAllSeqs);
1953 jMenu3.add(showAllhidden);
1954 hideMenu.add(hideSelColumns);
1955 hideMenu.add(hideSelSequences);
1956 hideMenu.add(hideAllSelection);
1957 hideMenu.add(hideAllButSelection);
1959 formatMenu.add(font);
1960 formatMenu.addSeparator();
1961 formatMenu.add(wrapMenuItem);
1962 formatMenu.add(scaleAbove);
1963 formatMenu.add(scaleLeft);
1964 formatMenu.add(scaleRight);
1965 formatMenu.add(seqLimits);
1966 formatMenu.add(idRightAlign);
1967 formatMenu.add(hiddenMarkers);
1968 formatMenu.add(viewBoxesMenuItem);
1969 formatMenu.add(viewTextMenuItem);
1970 formatMenu.add(colourTextMenuItem);
1971 formatMenu.add(renderGapsMenuItem);
1972 formatMenu.add(centreColumnLabelsMenuItem);
1973 formatMenu.add(showNonconservedMenuItem);
1974 selectMenu.add(findMenuItem);
1975 selectMenu.addSeparator();
1976 selectMenu.add(selectAllSequenceMenuItem);
1977 selectMenu.add(deselectAllSequenceMenuItem);
1978 selectMenu.add(invertSequenceMenuItem);
1979 selectMenu.add(invertColSel);
1980 selectMenu.add(createGroup);
1981 selectMenu.add(unGroup);
1982 selectMenu.add(grpsFromSelection);
1983 selectMenu.add(deleteGroups);
1984 calculateMenu.add(expandAlignment);
1985 // TODO - determine if the listenToViewSelections button is needed : see bug
1987 // selectMenu.addSeparator();
1988 // selectMenu.add(listenToViewSelections);
1991 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1993 // TODO Auto-generated method stub
1997 protected void listenToViewSelections_actionPerformed(ActionEvent e)
1999 // TODO Auto-generated method stub
2003 protected void showAllhidden_actionPerformed(ActionEvent e)
2005 // TODO Auto-generated method stub
2009 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2011 // TODO Auto-generated method stub
2015 protected void hideAllSelection_actionPerformed(ActionEvent e)
2017 // TODO Auto-generated method stub
2021 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2023 // TODO Auto-generated method stub
2027 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2029 // TODO Auto-generated method stub
2033 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2035 // TODO Auto-generated method stub
2039 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2041 // TODO Auto-generated method stub
2045 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2047 // TODO Auto-generated method stub
2051 protected void showGroupConservation_actionPerformed(ActionEvent e)
2053 // TODO Auto-generated method stub
2057 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2059 // TODO Auto-generated method stub
2063 protected void showSeqFeaturesHeight_actionPerformed(
2064 ActionEvent actionEvent)
2066 // TODO Auto-generated method stub
2070 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2072 // TODO Auto-generated method stub
2076 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2078 // TODO Auto-generated method stub
2082 protected void followHighlight_actionPerformed()
2084 // TODO Auto-generated method stub
2088 protected void showNpFeats_actionPerformed(ActionEvent e)
2090 // TODO Auto-generated method stub
2094 protected void showDbRefs_actionPerformed(ActionEvent e)
2096 // TODO Auto-generated method stub
2100 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2104 protected void showProducts_actionPerformed(ActionEvent e)
2108 protected void buildSortByAnnotationScoresMenu()
2112 protected void extractScores_actionPerformed(ActionEvent e)
2116 protected void outputText_actionPerformed(ActionEvent e)
2120 public void addFromFile_actionPerformed(ActionEvent e)
2125 public void addFromText_actionPerformed(ActionEvent e)
2130 public void addFromURL_actionPerformed(ActionEvent e)
2135 public void exportFeatures_actionPerformed(ActionEvent e)
2140 public void exportAnnotations_actionPerformed(ActionEvent e)
2145 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2149 protected void closeMenuItem_actionPerformed(boolean b)
2153 protected void redoMenuItem_actionPerformed(ActionEvent e)
2157 protected void undoMenuItem_actionPerformed(ActionEvent e)
2161 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2165 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2169 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2173 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2177 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2181 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2185 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2189 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2193 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2197 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2201 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2205 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2209 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2213 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2217 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2221 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2225 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2229 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2233 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2237 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2241 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2245 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2249 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2253 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2257 protected void clustalColour_actionPerformed(ActionEvent e)
2261 protected void zappoColour_actionPerformed(ActionEvent e)
2265 protected void taylorColour_actionPerformed(ActionEvent e)
2269 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2273 protected void helixColour_actionPerformed(ActionEvent e)
2277 protected void strandColour_actionPerformed(ActionEvent e)
2281 protected void turnColour_actionPerformed(ActionEvent e)
2285 protected void buriedColour_actionPerformed(ActionEvent e)
2289 protected void userDefinedColour_actionPerformed(ActionEvent e)
2293 protected void PIDColour_actionPerformed(ActionEvent e)
2297 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2301 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2306 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2309 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2313 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2317 protected void printMenuItem_actionPerformed(ActionEvent e)
2321 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2325 protected void findMenuItem_actionPerformed(ActionEvent e)
2329 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2333 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2337 protected void nucleotideColour_actionPerformed(ActionEvent e)
2341 protected void deleteGroups_actionPerformed(ActionEvent e)
2345 protected void createGroup_actionPerformed(ActionEvent e)
2349 protected void unGroup_actionPerformed(ActionEvent e)
2353 protected void copy_actionPerformed(ActionEvent e)
2357 protected void cut_actionPerformed(ActionEvent e)
2361 protected void delete_actionPerformed(ActionEvent e)
2365 protected void pasteNew_actionPerformed(ActionEvent e)
2369 protected void pasteThis_actionPerformed(ActionEvent e)
2373 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2377 public void createPNG(java.io.File f)
2381 protected void font_actionPerformed(ActionEvent e)
2385 protected void seqLimit_actionPerformed(ActionEvent e)
2389 public void seqDBRef_actionPerformed(ActionEvent e)
2394 public void createEPS(java.io.File f)
2398 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2404 * Template method to handle the 'load T-Coffee scores' menu event.
2406 * Subclasses override this method to provide a custom action.
2411 protected void loadScores_actionPerformed(ActionEvent event)
2417 * Template method to handle the 'Color T-Coffee scores' menu event.
2419 * Subclasses override this method to provide a custom action.
2424 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2429 protected void jpred_actionPerformed(ActionEvent e)
2433 protected void scaleAbove_actionPerformed(ActionEvent e)
2437 protected void scaleLeft_actionPerformed(ActionEvent e)
2441 protected void scaleRight_actionPerformed(ActionEvent e)
2445 protected void modifyPID_actionPerformed(ActionEvent e)
2449 protected void modifyConservation_actionPerformed(ActionEvent e)
2453 protected void saveAs_actionPerformed(ActionEvent e)
2457 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2461 public void vamsasStore_actionPerformed(ActionEvent e)
2466 public void vamsasLoad_actionPerformed(ActionEvent e)
2471 public void showTranslation_actionPerformed(ActionEvent e)
2476 public void featureSettings_actionPerformed(ActionEvent e)
2481 public void fetchSequence_actionPerformed(ActionEvent e)
2486 public void smoothFont_actionPerformed(ActionEvent e)
2491 public void annotationColour_actionPerformed(ActionEvent e)
2496 public void rnahelicesColour_actionPerformed(ActionEvent e)
2501 public void associatedData_actionPerformed(ActionEvent e)
2506 public void autoCalculate_actionPerformed(ActionEvent e)
2511 public void sortByTreeOption_actionPerformed(ActionEvent e)
2516 public void showAllSeqs_actionPerformed(ActionEvent e)
2521 public void showAllColumns_actionPerformed(ActionEvent e)
2526 public void hideSelSequences_actionPerformed(ActionEvent e)
2531 public void hideSelColumns_actionPerformed(ActionEvent e)
2536 public void hiddenMarkers_actionPerformed(ActionEvent e)
2541 public void findPdbId_actionPerformed(ActionEvent e)
2546 public void enterPdbId_actionPerformed(ActionEvent e)
2551 public void pdbFile_actionPerformed(ActionEvent e)
2556 public void invertColSel_actionPerformed(ActionEvent e)
2561 public void tabSelectionChanged(int sel)
2566 public void tabbedPane_mousePressed(MouseEvent e)
2571 public void tabbedPane_focusGained(FocusEvent e)
2576 public void save_actionPerformed(ActionEvent e)
2581 public void reload_actionPerformed(ActionEvent e)
2586 public void newView_actionPerformed(ActionEvent e)
2591 public void textColour_actionPerformed(ActionEvent e)
2596 public void idRightAlign_actionPerformed(ActionEvent e)
2601 public void expandViews_actionPerformed(ActionEvent e)
2606 public void gatherViews_actionPerformed(ActionEvent e)
2611 public void buildTreeMenu()
2616 public void pageSetup_actionPerformed(ActionEvent e)
2621 public void alignmentProperties()
2626 protected void expand_newalign(ActionEvent e)
2628 // TODO Auto-generated method stub