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.setToolTipText(MessageManager.getString("label.view_flanking_regions"));
637 expandAlignment.addActionListener(new java.awt.event.ActionListener() {
639 public void actionPerformed(ActionEvent e)
644 remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
645 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
646 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
647 .getMenuShortcutKeyMask(), false));
649 .addActionListener(new java.awt.event.ActionListener()
651 public void actionPerformed(ActionEvent e)
653 remove2LeftMenuItem_actionPerformed(e);
656 remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
657 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
658 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
659 .getMenuShortcutKeyMask(), false));
661 .addActionListener(new java.awt.event.ActionListener()
663 public void actionPerformed(ActionEvent e)
665 remove2RightMenuItem_actionPerformed(e);
668 removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
669 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
670 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
671 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
672 removeGappedColumnMenuItem
673 .addActionListener(new java.awt.event.ActionListener()
675 public void actionPerformed(ActionEvent e)
677 removeGappedColumnMenuItem_actionPerformed(e);
680 removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
681 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
682 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
683 .getDefaultToolkit().getMenuShortcutKeyMask()
684 | java.awt.event.KeyEvent.SHIFT_MASK, false));
685 removeAllGapsMenuItem
686 .addActionListener(new java.awt.event.ActionListener()
688 public void actionPerformed(ActionEvent e)
690 removeAllGapsMenuItem_actionPerformed(e);
693 justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
695 .addActionListener(new java.awt.event.ActionListener()
697 public void actionPerformed(ActionEvent e)
699 justifyLeftMenuItem_actionPerformed(e);
702 justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
704 .addActionListener(new java.awt.event.ActionListener()
706 public void actionPerformed(ActionEvent e)
708 justifyRightMenuItem_actionPerformed(e);
711 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
712 viewBoxesMenuItem.setState(true);
713 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
715 public void actionPerformed(ActionEvent e)
717 viewBoxesMenuItem_actionPerformed(e);
720 viewTextMenuItem.setText(MessageManager.getString("action.text"));
721 viewTextMenuItem.setState(true);
722 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
724 public void actionPerformed(ActionEvent e)
726 viewTextMenuItem_actionPerformed(e);
729 showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
730 showNonconservedMenuItem.setState(false);
731 showNonconservedMenuItem
732 .addActionListener(new java.awt.event.ActionListener()
734 public void actionPerformed(ActionEvent e)
736 showUnconservedMenuItem_actionPerformed(e);
739 sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
741 .addActionListener(new java.awt.event.ActionListener()
743 public void actionPerformed(ActionEvent e)
745 sortPairwiseMenuItem_actionPerformed(e);
748 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
749 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
751 public void actionPerformed(ActionEvent e)
753 sortIDMenuItem_actionPerformed(e);
756 sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
758 .addActionListener(new java.awt.event.ActionListener()
760 public void actionPerformed(ActionEvent e)
762 sortLengthMenuItem_actionPerformed(e);
765 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
766 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
768 public void actionPerformed(ActionEvent e)
770 sortGroupMenuItem_actionPerformed(e);
773 removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
774 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
775 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
776 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
777 removeRedundancyMenuItem
778 .addActionListener(new java.awt.event.ActionListener()
780 public void actionPerformed(ActionEvent e)
782 removeRedundancyMenuItem_actionPerformed(e);
785 pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
786 pairwiseAlignmentMenuItem
787 .addActionListener(new java.awt.event.ActionListener()
789 public void actionPerformed(ActionEvent e)
791 pairwiseAlignmentMenuItem_actionPerformed(e);
794 PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
795 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
797 public void actionPerformed(ActionEvent e)
799 PCAMenuItem_actionPerformed(e);
802 averageDistanceTreeMenuItem
803 .setText(MessageManager.getString("label.average_distance_identity"));
804 averageDistanceTreeMenuItem
805 .addActionListener(new java.awt.event.ActionListener()
807 public void actionPerformed(ActionEvent e)
809 averageDistanceTreeMenuItem_actionPerformed(e);
812 neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
813 neighbourTreeMenuItem
814 .addActionListener(new java.awt.event.ActionListener()
816 public void actionPerformed(ActionEvent e)
818 neighbourTreeMenuItem_actionPerformed(e);
821 this.getContentPane().setLayout(borderLayout1);
822 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
823 statusBar.setBackground(Color.white);
824 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
825 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
826 statusBar.setText(MessageManager.getString("label.status_bar"));
827 outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
828 clustalColour.setText(MessageManager.getString("label.clustalx"));
830 clustalColour.addActionListener(new java.awt.event.ActionListener()
832 public void actionPerformed(ActionEvent e)
834 clustalColour_actionPerformed(e);
837 zappoColour.setText(MessageManager.getString("label.zappo"));
838 zappoColour.addActionListener(new java.awt.event.ActionListener()
840 public void actionPerformed(ActionEvent e)
842 zappoColour_actionPerformed(e);
845 taylorColour.setText(MessageManager.getString("label.taylor"));
846 taylorColour.addActionListener(new java.awt.event.ActionListener()
848 public void actionPerformed(ActionEvent e)
850 taylorColour_actionPerformed(e);
853 hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
855 .addActionListener(new java.awt.event.ActionListener()
857 public void actionPerformed(ActionEvent e)
859 hydrophobicityColour_actionPerformed(e);
862 helixColour.setText(MessageManager.getString("label.helix_propensity"));
863 helixColour.addActionListener(new java.awt.event.ActionListener()
865 public void actionPerformed(ActionEvent e)
867 helixColour_actionPerformed(e);
870 strandColour.setText(MessageManager.getString("label.strand_propensity"));
871 strandColour.addActionListener(new java.awt.event.ActionListener()
873 public void actionPerformed(ActionEvent e)
875 strandColour_actionPerformed(e);
878 turnColour.setText(MessageManager.getString("label.turn_propensity"));
879 turnColour.addActionListener(new java.awt.event.ActionListener()
881 public void actionPerformed(ActionEvent e)
883 turnColour_actionPerformed(e);
886 buriedColour.setText(MessageManager.getString("label.buried_index"));
887 buriedColour.addActionListener(new java.awt.event.ActionListener()
889 public void actionPerformed(ActionEvent e)
891 buriedColour_actionPerformed(e);
894 userDefinedColour.setText(MessageManager.getString("action.user_defined"));
895 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
897 public void actionPerformed(ActionEvent e)
899 userDefinedColour_actionPerformed(e);
902 PIDColour.setText(MessageManager.getString("label.percentage_identity"));
903 PIDColour.addActionListener(new java.awt.event.ActionListener()
905 public void actionPerformed(ActionEvent e)
907 PIDColour_actionPerformed(e);
910 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
911 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
913 public void actionPerformed(ActionEvent e)
915 BLOSUM62Colour_actionPerformed(e);
918 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
919 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
921 public void actionPerformed(ActionEvent e)
923 nucleotideColour_actionPerformed(e);
927 purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
928 purinePyrimidineColour
929 .addActionListener(new java.awt.event.ActionListener()
931 public void actionPerformed(ActionEvent e)
933 purinePyrimidineColour_actionPerformed(e);
937 * covariationColour.setText("Covariation");
938 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
939 * public void actionPerformed(ActionEvent e) {
940 * covariationColour_actionPerformed(e); } });
943 avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
944 avDistanceTreeBlosumMenuItem
945 .addActionListener(new java.awt.event.ActionListener()
947 public void actionPerformed(ActionEvent e)
949 avTreeBlosumMenuItem_actionPerformed(e);
952 njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
954 .addActionListener(new java.awt.event.ActionListener()
956 public void actionPerformed(ActionEvent e)
958 njTreeBlosumMenuItem_actionPerformed(e);
961 annotationPanelMenuItem.setActionCommand("");
962 annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
963 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
964 "SHOW_ANNOTATIONS", true));
965 annotationPanelMenuItem
966 .addActionListener(new java.awt.event.ActionListener()
968 public void actionPerformed(ActionEvent e)
970 annotationPanelMenuItem_actionPerformed(e);
973 colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
975 .addActionListener(new java.awt.event.ActionListener()
977 public void actionPerformed(ActionEvent e)
979 colourTextMenuItem_actionPerformed(e);
982 htmlMenuItem.setText(MessageManager.getString("label.html"));
983 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
985 public void actionPerformed(ActionEvent e)
987 htmlMenuItem_actionPerformed(e);
990 overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
991 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
993 public void actionPerformed(ActionEvent e)
995 overviewMenuItem_actionPerformed(e);
998 undoMenuItem.setEnabled(false);
999 undoMenuItem.setText(MessageManager.getString("action.undo"));
1000 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1001 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1002 .getMenuShortcutKeyMask(), false));
1003 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 undoMenuItem_actionPerformed(e);
1010 redoMenuItem.setEnabled(false);
1011 redoMenuItem.setText(MessageManager.getString("action.redo"));
1012 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1013 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1014 .getMenuShortcutKeyMask(), false));
1015 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1017 public void actionPerformed(ActionEvent e)
1019 redoMenuItem_actionPerformed(e);
1022 conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
1023 conservationMenuItem
1024 .addActionListener(new java.awt.event.ActionListener()
1026 public void actionPerformed(ActionEvent e)
1028 conservationMenuItem_actionPerformed(e);
1031 noColourmenuItem.setText(MessageManager.getString("label.none"));
1032 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1034 public void actionPerformed(ActionEvent e)
1036 noColourmenuItem_actionPerformed(e);
1039 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1040 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 wrapMenuItem_actionPerformed(e);
1047 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1048 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1049 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1050 .getMenuShortcutKeyMask(), false));
1051 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1053 public void actionPerformed(ActionEvent e)
1055 printMenuItem_actionPerformed(e);
1058 renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
1059 renderGapsMenuItem.setState(true);
1061 .addActionListener(new java.awt.event.ActionListener()
1063 public void actionPerformed(ActionEvent e)
1065 renderGapsMenuItem_actionPerformed(e);
1068 findMenuItem.setText(MessageManager.getString("action.find"));
1069 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1070 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1071 .getMenuShortcutKeyMask(), false));
1072 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1074 public void actionPerformed(ActionEvent e)
1076 findMenuItem_actionPerformed(e);
1079 abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
1080 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1082 public void actionPerformed(ActionEvent e)
1084 abovePIDThreshold_actionPerformed(e);
1087 showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
1088 showSeqFeatures.addActionListener(new ActionListener()
1090 public void actionPerformed(ActionEvent actionEvent)
1092 showSeqFeatures_actionPerformed(actionEvent);
1096 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1097 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1098 * void actionPerformed(ActionEvent actionEvent) {
1099 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1101 showDbRefsMenuitem.setText(MessageManager.getString("label.show_database_refs"));
1102 showDbRefsMenuitem.addActionListener(new ActionListener()
1105 public void actionPerformed(ActionEvent e)
1107 showDbRefs_actionPerformed(e);
1111 showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
1112 showNpFeatsMenuitem.addActionListener(new ActionListener()
1115 public void actionPerformed(ActionEvent e)
1117 showNpFeats_actionPerformed(e);
1121 showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
1122 showGroupConservation.addActionListener(new ActionListener()
1125 public void actionPerformed(ActionEvent e)
1127 showGroupConservation_actionPerformed(e);
1132 showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
1133 showGroupConsensus.addActionListener(new ActionListener()
1136 public void actionPerformed(ActionEvent e)
1138 showGroupConsensus_actionPerformed(e);
1142 showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
1143 showConsensusHistogram.addActionListener(new ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 showConsensusHistogram_actionPerformed(e);
1152 showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
1153 showSequenceLogo.addActionListener(new ActionListener()
1156 public void actionPerformed(ActionEvent e)
1158 showSequenceLogo_actionPerformed(e);
1162 normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
1163 normaliseSequenceLogo.addActionListener(new ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 normaliseSequenceLogo_actionPerformed(e);
1172 applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
1173 applyAutoAnnotationSettings.setState(false);
1174 applyAutoAnnotationSettings.setVisible(true);
1175 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1178 public void actionPerformed(ActionEvent e)
1180 applyAutoAnnotationSettings_actionPerformed(e);
1185 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1186 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 nucleotideColour_actionPerformed(e);
1194 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1195 tcoffeeColour.setEnabled(false);
1196 tcoffeeColour.addActionListener(new ActionListener()
1200 public void actionPerformed(ActionEvent e)
1202 tcoffeeColorScheme_actionPerformed(e);
1206 deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
1207 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1208 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1209 .getMenuShortcutKeyMask(), false));
1210 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1212 public void actionPerformed(ActionEvent e)
1214 deleteGroups_actionPerformed(e);
1217 createGroup.setText(MessageManager.getString("action.create_groups"));
1218 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1219 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1220 .getMenuShortcutKeyMask(), false));
1221 createGroup.addActionListener(new java.awt.event.ActionListener()
1223 public void actionPerformed(ActionEvent e)
1225 createGroup_actionPerformed(e);
1228 unGroup.setText(MessageManager.getString("action.remove_group"));
1229 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1230 java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
1231 .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
1232 unGroup.addActionListener(new java.awt.event.ActionListener()
1234 public void actionPerformed(ActionEvent e)
1236 unGroup_actionPerformed(e);
1239 copy.setText(MessageManager.getString("action.copy"));
1240 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1241 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1242 .getMenuShortcutKeyMask(), false));
1244 copy.addActionListener(new java.awt.event.ActionListener()
1246 public void actionPerformed(ActionEvent e)
1248 copy_actionPerformed(e);
1251 cut.setText(MessageManager.getString("action.cut"));
1252 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1253 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1254 .getMenuShortcutKeyMask(), false));
1255 cut.addActionListener(new java.awt.event.ActionListener()
1257 public void actionPerformed(ActionEvent e)
1259 cut_actionPerformed(e);
1262 delete.setText(MessageManager.getString("action.delete"));
1263 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1264 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1265 delete.addActionListener(new java.awt.event.ActionListener()
1267 public void actionPerformed(ActionEvent e)
1269 delete_actionPerformed(e);
1272 pasteMenu.setText(MessageManager.getString("action.paste"));
1273 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1274 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1275 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1276 .getMenuShortcutKeyMask()
1277 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1278 pasteNew.addActionListener(new java.awt.event.ActionListener()
1280 public void actionPerformed(ActionEvent e)
1282 pasteNew_actionPerformed(e);
1285 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1286 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1287 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1288 .getMenuShortcutKeyMask(), false));
1289 pasteThis.addActionListener(new java.awt.event.ActionListener()
1291 public void actionPerformed(ActionEvent e)
1293 pasteThis_actionPerformed(e);
1296 applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
1297 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1299 public void actionPerformed(ActionEvent e)
1301 applyToAllGroups_actionPerformed(e);
1304 createPNG.addActionListener(new java.awt.event.ActionListener()
1306 public void actionPerformed(ActionEvent e)
1311 createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
1312 createPNG.setText("PNG");
1313 font.setText(MessageManager.getString("action.font"));
1314 font.addActionListener(new java.awt.event.ActionListener()
1316 public void actionPerformed(ActionEvent e)
1318 font_actionPerformed(e);
1322 seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
1323 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1324 seqLimits.addActionListener(new java.awt.event.ActionListener()
1326 public void actionPerformed(ActionEvent e)
1328 seqLimit_actionPerformed(e);
1331 epsFile.setText("EPS");
1332 epsFile.addActionListener(new java.awt.event.ActionListener()
1334 public void actionPerformed(ActionEvent e)
1339 LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
1340 LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree"));
1341 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1343 public void actionPerformed(ActionEvent e)
1345 LoadtreeMenuItem_actionPerformed(e);
1349 scaleAbove.setVisible(false);
1350 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1351 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1353 public void actionPerformed(ActionEvent e)
1355 scaleAbove_actionPerformed(e);
1358 scaleLeft.setVisible(false);
1359 scaleLeft.setSelected(true);
1360 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1361 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1363 public void actionPerformed(ActionEvent e)
1365 scaleLeft_actionPerformed(e);
1368 scaleRight.setVisible(false);
1369 scaleRight.setSelected(true);
1370 scaleRight.setText(MessageManager.getString("action.scale_right"));
1371 scaleRight.addActionListener(new java.awt.event.ActionListener()
1373 public void actionPerformed(ActionEvent e)
1375 scaleRight_actionPerformed(e);
1378 centreColumnLabelsMenuItem.setVisible(true);
1379 centreColumnLabelsMenuItem.setState(false);
1380 centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
1381 centreColumnLabelsMenuItem
1382 .addActionListener(new java.awt.event.ActionListener()
1384 public void actionPerformed(ActionEvent e)
1386 centreColumnLabels_actionPerformed(e);
1389 followHighlightMenuItem.setVisible(true);
1390 followHighlightMenuItem.setState(true);
1391 followHighlightMenuItem.setText(MessageManager.getString("label.automatic_scrolling"));
1392 followHighlightMenuItem.addActionListener(new ActionListener()
1395 public void actionPerformed(ActionEvent e)
1397 followHighlight_actionPerformed();
1402 modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
1403 modifyPID.addActionListener(new java.awt.event.ActionListener()
1405 public void actionPerformed(ActionEvent e)
1407 modifyPID_actionPerformed(e);
1410 modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
1412 .addActionListener(new java.awt.event.ActionListener()
1414 public void actionPerformed(ActionEvent e)
1416 modifyConservation_actionPerformed(e);
1419 sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order"));
1420 sort.setText(MessageManager.getString("action.sort"));
1421 sort.addMenuListener(new MenuListener()
1423 public void menuSelected(MenuEvent e)
1428 public void menuDeselected(MenuEvent e)
1432 public void menuCanceled(MenuEvent e)
1436 sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
1437 sort.add(sortByAnnotScore);
1438 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1441 public void menuCanceled(MenuEvent e)
1445 public void menuDeselected(MenuEvent e)
1449 public void menuSelected(MenuEvent e)
1451 buildSortByAnnotationScoresMenu();
1454 sortByAnnotScore.setVisible(false);
1456 calculateTree.setText(MessageManager.getString("action.calculate_tree"));
1458 jMenu2.setText(MessageManager.getString("label.export_image"));
1459 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1460 padGapsMenuitem.setState(jalview.bin.Cache
1461 .getDefault("PAD_GAPS", false));
1462 padGapsMenuitem.addActionListener(new ActionListener()
1464 public void actionPerformed(ActionEvent e)
1466 padGapsMenuitem_actionPerformed(e);
1469 vamsasStore.setVisible(false);
1470 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1471 vamsasStore.addActionListener(new ActionListener()
1473 public void actionPerformed(ActionEvent e)
1475 vamsasStore_actionPerformed(e);
1478 showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
1479 showTranslation.addActionListener(new ActionListener()
1481 public void actionPerformed(ActionEvent e)
1483 showTranslation_actionPerformed(e);
1486 extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
1487 extractScores.addActionListener(new ActionListener()
1489 public void actionPerformed(ActionEvent e)
1491 extractScores_actionPerformed(e);
1494 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1496 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1498 * showProducts.addActionListener(new ActionListener() {
1500 * public void actionPerformed(ActionEvent e) {
1501 * showProducts_actionPerformed(e); } });
1503 openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
1504 openFeatureSettings.addActionListener(new ActionListener()
1506 public void actionPerformed(ActionEvent e)
1508 featureSettings_actionPerformed(e);
1511 fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
1512 fetchSequence.addActionListener(new ActionListener()
1514 public void actionPerformed(ActionEvent e)
1516 fetchSequence_actionPerformed(e);
1520 annotationColour.setText(MessageManager.getString("action.by_annotation"));
1521 annotationColour.addActionListener(new ActionListener()
1523 public void actionPerformed(ActionEvent e)
1525 annotationColour_actionPerformed(e);
1529 rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
1530 rnahelicesColour.addActionListener(new ActionListener()
1532 public void actionPerformed(ActionEvent e)
1534 rnahelicesColour_actionPerformed(e);
1538 associatedData.setText(MessageManager.getString("label.load_features_annotations"));
1539 associatedData.addActionListener(new ActionListener()
1541 public void actionPerformed(ActionEvent e)
1543 associatedData_actionPerformed(e);
1546 autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
1547 autoCalculate.setState(jalview.bin.Cache.getDefault(
1548 "AUTO_CALC_CONSENSUS", true));
1549 autoCalculate.addActionListener(new ActionListener()
1551 public void actionPerformed(ActionEvent e)
1553 autoCalculate_actionPerformed(e);
1556 sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
1558 .setToolTipText("<html>" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1560 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1561 sortByTree.addActionListener(new ActionListener()
1563 public void actionPerformed(ActionEvent e)
1565 sortByTreeOption_actionPerformed(e);
1569 listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
1570 listenToViewSelections
1571 .setToolTipText("<html>" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1572 listenToViewSelections.setState(false);
1573 listenToViewSelections.addActionListener(new ActionListener()
1575 public void actionPerformed(ActionEvent e)
1577 listenToViewSelections_actionPerformed(e);
1581 addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
1582 addFromFile.setText(MessageManager.getString("label.from_file"));
1583 addFromFile.addActionListener(new ActionListener()
1585 public void actionPerformed(ActionEvent e)
1587 addFromFile_actionPerformed(e);
1590 addFromText.setText(MessageManager.getString("label.from_textbox"));
1591 addFromText.addActionListener(new ActionListener()
1593 public void actionPerformed(ActionEvent e)
1595 addFromText_actionPerformed(e);
1598 addFromURL.setText(MessageManager.getString("label.from_url"));
1599 addFromURL.addActionListener(new ActionListener()
1601 public void actionPerformed(ActionEvent e)
1603 addFromURL_actionPerformed(e);
1606 exportFeatures.setText(MessageManager.getString("label.export_features"));
1607 exportFeatures.addActionListener(new ActionListener()
1609 public void actionPerformed(ActionEvent e)
1611 exportFeatures_actionPerformed(e);
1614 exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
1615 exportAnnotations.addActionListener(new ActionListener()
1617 public void actionPerformed(ActionEvent e)
1619 exportAnnotations_actionPerformed(e);
1622 statusPanel.setLayout(gridLayout1);
1623 jMenu3.setText(MessageManager.getString("action.show"));
1624 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1625 showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1626 showAllSeqs.addActionListener(new ActionListener()
1628 public void actionPerformed(ActionEvent e)
1630 showAllSeqs_actionPerformed(e);
1633 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1634 showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1635 showAllColumns.addActionListener(new ActionListener()
1637 public void actionPerformed(ActionEvent e)
1639 showAllColumns_actionPerformed(e);
1642 hideMenu.setText(MessageManager.getString("action.hide"));
1643 hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
1644 hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1645 hideSelSequences.addActionListener(new ActionListener()
1647 public void actionPerformed(ActionEvent e)
1649 hideSelSequences_actionPerformed(e);
1652 hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
1653 hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1654 hideSelColumns.addActionListener(new ActionListener()
1656 public void actionPerformed(ActionEvent e)
1658 hideSelColumns_actionPerformed(e);
1661 hideAllSelection.setText(MessageManager.getString("label.selected_region"));
1662 hideAllSelection.addActionListener(new ActionListener()
1664 public void actionPerformed(ActionEvent e)
1666 hideAllSelection_actionPerformed(e);
1669 // TODO: should be hidden if no selection exists.
1670 hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
1671 hideAllButSelection.addActionListener(new ActionListener()
1673 public void actionPerformed(ActionEvent e)
1675 hideAllButSelection_actionPerformed(e);
1678 showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
1680 .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
1681 showAllhidden.addActionListener(new ActionListener()
1683 public void actionPerformed(ActionEvent e)
1685 showAllhidden_actionPerformed(e);
1689 hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
1690 hiddenMarkers.addActionListener(new ActionListener()
1692 public void actionPerformed(ActionEvent e)
1694 hiddenMarkers_actionPerformed(e);
1697 invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
1698 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1699 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1700 .getMenuShortcutKeyMask()
1701 | java.awt.event.KeyEvent.ALT_MASK, false));
1702 invertColSel.addActionListener(new ActionListener()
1704 public void actionPerformed(ActionEvent e)
1706 invertColSel_actionPerformed(e);
1709 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1711 public void stateChanged(ChangeEvent evt)
1713 JTabbedPane pane = (JTabbedPane) evt.getSource();
1714 int sel = pane.getSelectedIndex();
1715 tabSelectionChanged(sel);
1718 tabbedPane.addMouseListener(new MouseAdapter()
1720 public void mousePressed(MouseEvent e)
1722 tabbedPane_mousePressed(e);
1725 tabbedPane.addFocusListener(new FocusAdapter()
1727 public void focusGained(FocusEvent e)
1729 tabbedPane_focusGained(e);
1732 save.setText(MessageManager.getString("action.save"));
1733 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1734 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1735 .getMenuShortcutKeyMask(), false));
1736 save.addActionListener(new ActionListener()
1738 public void actionPerformed(ActionEvent e)
1740 save_actionPerformed(e);
1743 reload.setEnabled(false);
1744 reload.setText(MessageManager.getString("action.reload"));
1745 reload.addActionListener(new ActionListener()
1747 public void actionPerformed(ActionEvent e)
1749 reload_actionPerformed(e);
1752 newView.setText(MessageManager.getString("action.new_view"));
1753 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1754 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1755 .getMenuShortcutKeyMask(), false));
1756 newView.addActionListener(new ActionListener()
1758 public void actionPerformed(ActionEvent e)
1760 newView_actionPerformed(e);
1763 tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
1764 textColour.setText(MessageManager.getString("label.colour_text") + "...");
1765 textColour.addActionListener(new ActionListener()
1767 public void actionPerformed(ActionEvent e)
1769 textColour_actionPerformed(e);
1772 formatMenu.setText(MessageManager.getString("action.format"));
1773 selectMenu.setText(MessageManager.getString("action.select"));
1774 idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id"));
1775 idRightAlign.addActionListener(new ActionListener()
1777 public void actionPerformed(ActionEvent e)
1779 idRightAlign_actionPerformed(e);
1782 gatherViews.setEnabled(false);
1783 gatherViews.setText(MessageManager.getString("action.gather_views"));
1784 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1785 java.awt.event.KeyEvent.VK_G, 0, false));
1786 gatherViews.addActionListener(new ActionListener()
1788 public void actionPerformed(ActionEvent e)
1790 gatherViews_actionPerformed(e);
1793 expandViews.setEnabled(false);
1794 expandViews.setText(MessageManager.getString("action.expand_views"));
1795 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1796 java.awt.event.KeyEvent.VK_X, 0, false));
1797 expandViews.addActionListener(new ActionListener()
1799 public void actionPerformed(ActionEvent e)
1801 expandViews_actionPerformed(e);
1804 pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
1805 pageSetup.addActionListener(new ActionListener()
1807 public void actionPerformed(ActionEvent e)
1809 pageSetup_actionPerformed(e);
1812 alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
1813 alignmentProperties.addActionListener(new ActionListener()
1815 public void actionPerformed(ActionEvent actionEvent)
1817 alignmentProperties();
1820 tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
1821 autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
1822 alignFrameMenuBar.add(fileMenu);
1823 alignFrameMenuBar.add(editMenu);
1824 alignFrameMenuBar.add(selectMenu);
1825 alignFrameMenuBar.add(viewMenu);
1826 alignFrameMenuBar.add(formatMenu);
1827 alignFrameMenuBar.add(colourMenu);
1828 alignFrameMenuBar.add(calculateMenu);
1829 alignFrameMenuBar.add(webService);
1830 fileMenu.add(fetchSequence);
1831 fileMenu.add(addSequenceMenu);
1832 fileMenu.add(reload);
1833 fileMenu.addSeparator();
1834 fileMenu.add(vamsasStore);
1836 fileMenu.add(saveAs);
1837 fileMenu.add(outputTextboxMenu);
1838 fileMenu.add(pageSetup);
1839 fileMenu.add(printMenuItem);
1840 fileMenu.addSeparator();
1841 fileMenu.add(jMenu2);
1842 fileMenu.add(exportFeatures);
1843 fileMenu.add(exportAnnotations);
1844 fileMenu.add(LoadtreeMenuItem);
1845 fileMenu.add(associatedData);
1846 fileMenu.addSeparator();
1847 fileMenu.add(closeMenuItem);
1848 editMenu.add(undoMenuItem);
1849 editMenu.add(redoMenuItem);
1852 editMenu.add(pasteMenu);
1853 editMenu.add(delete);
1854 editMenu.addSeparator();
1855 editMenu.add(remove2LeftMenuItem);
1856 editMenu.add(remove2RightMenuItem);
1857 editMenu.add(removeGappedColumnMenuItem);
1858 editMenu.add(removeAllGapsMenuItem);
1859 editMenu.add(removeRedundancyMenuItem);
1860 editMenu.addSeparator();
1861 // dont add these yet in the CVS build - they cannot be undone!
1862 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1863 // editMenu.add(justifyLeftMenuItem);
1864 // editMenu.add(justifyRightMenuItem);
1865 // editMenu.addSeparator();
1866 editMenu.add(padGapsMenuitem);
1867 viewMenu.add(newView);
1868 viewMenu.add(expandViews);
1869 viewMenu.add(gatherViews);
1870 viewMenu.addSeparator();
1871 viewMenu.add(jMenu3);
1872 viewMenu.add(hideMenu);
1873 viewMenu.addSeparator();
1874 viewMenu.add(followHighlightMenuItem);
1875 viewMenu.add(annotationPanelMenuItem);
1876 autoAnnMenu.add(applyAutoAnnotationSettings);
1877 autoAnnMenu.add(showConsensusHistogram);
1878 autoAnnMenu.add(showSequenceLogo);
1879 autoAnnMenu.add(normaliseSequenceLogo);
1880 autoAnnMenu.addSeparator();
1881 autoAnnMenu.add(showGroupConservation);
1882 autoAnnMenu.add(showGroupConsensus);
1883 viewMenu.add(autoAnnMenu);
1884 viewMenu.addSeparator();
1885 viewMenu.add(showSeqFeatures);
1886 // viewMenu.add(showSeqFeaturesHeight);
1888 viewMenu.add(openFeatureSettings);
1889 tooltipSettingsMenu.add(showDbRefsMenuitem);
1890 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1891 viewMenu.add(tooltipSettingsMenu);
1892 viewMenu.addSeparator();
1893 viewMenu.add(alignmentProperties);
1894 viewMenu.addSeparator();
1895 viewMenu.add(overviewMenuItem);
1896 colourMenu.add(applyToAllGroups);
1897 colourMenu.add(textColour);
1898 colourMenu.addSeparator();
1899 colourMenu.add(noColourmenuItem);
1900 colourMenu.add(clustalColour);
1901 colourMenu.add(BLOSUM62Colour);
1902 colourMenu.add(PIDColour);
1903 colourMenu.add(zappoColour);
1904 colourMenu.add(taylorColour);
1905 colourMenu.add(hydrophobicityColour);
1906 colourMenu.add(helixColour);
1907 colourMenu.add(strandColour);
1908 colourMenu.add(turnColour);
1909 colourMenu.add(buriedColour);
1910 colourMenu.add(nucleotideColour);
1911 colourMenu.add(purinePyrimidineColour);
1912 // colourMenu.add(covariationColour);
1913 colourMenu.add(tcoffeeColour);
1914 colourMenu.add(userDefinedColour);
1915 colourMenu.addSeparator();
1916 colourMenu.add(conservationMenuItem);
1917 colourMenu.add(modifyConservation);
1918 colourMenu.add(abovePIDThreshold);
1919 colourMenu.add(modifyPID);
1920 colourMenu.add(annotationColour);
1921 colourMenu.add(rnahelicesColour);
1922 calculateMenu.add(sort);
1923 calculateMenu.add(calculateTree);
1924 calculateMenu.addSeparator();
1925 calculateMenu.add(pairwiseAlignmentMenuItem);
1926 calculateMenu.add(PCAMenuItem);
1927 calculateMenu.addSeparator();
1928 calculateMenu.add(showTranslation);
1929 calculateMenu.add(showProducts);
1930 calculateMenu.add(autoCalculate);
1931 calculateMenu.add(sortByTree);
1932 calculateMenu.addSeparator();
1933 calculateMenu.add(extractScores);
1934 webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
1935 webService.add(webServiceNoServices);
1936 pasteMenu.add(pasteNew);
1937 pasteMenu.add(pasteThis);
1938 sort.add(sortIDMenuItem);
1939 sort.add(sortLengthMenuItem);
1940 sort.add(sortGroupMenuItem);
1941 sort.add(sortPairwiseMenuItem);
1942 sort.add(sortByTreeMenu);
1943 jMenu2.add(htmlMenuItem);
1944 jMenu2.add(epsFile);
1945 jMenu2.add(createPNG);
1946 addSequenceMenu.add(addFromFile);
1947 addSequenceMenu.add(addFromText);
1948 addSequenceMenu.add(addFromURL);
1949 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1950 statusPanel.add(statusBar, null);
1951 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1952 jMenu3.add(showAllColumns);
1953 jMenu3.add(showAllSeqs);
1954 jMenu3.add(showAllhidden);
1955 hideMenu.add(hideSelColumns);
1956 hideMenu.add(hideSelSequences);
1957 hideMenu.add(hideAllSelection);
1958 hideMenu.add(hideAllButSelection);
1960 formatMenu.add(font);
1961 formatMenu.addSeparator();
1962 formatMenu.add(wrapMenuItem);
1963 formatMenu.add(scaleAbove);
1964 formatMenu.add(scaleLeft);
1965 formatMenu.add(scaleRight);
1966 formatMenu.add(seqLimits);
1967 formatMenu.add(idRightAlign);
1968 formatMenu.add(hiddenMarkers);
1969 formatMenu.add(viewBoxesMenuItem);
1970 formatMenu.add(viewTextMenuItem);
1971 formatMenu.add(colourTextMenuItem);
1972 formatMenu.add(renderGapsMenuItem);
1973 formatMenu.add(centreColumnLabelsMenuItem);
1974 formatMenu.add(showNonconservedMenuItem);
1975 selectMenu.add(findMenuItem);
1976 selectMenu.addSeparator();
1977 selectMenu.add(selectAllSequenceMenuItem);
1978 selectMenu.add(deselectAllSequenceMenuItem);
1979 selectMenu.add(invertSequenceMenuItem);
1980 selectMenu.add(invertColSel);
1981 selectMenu.add(createGroup);
1982 selectMenu.add(unGroup);
1983 selectMenu.add(grpsFromSelection);
1984 selectMenu.add(deleteGroups);
1985 calculateMenu.add(expandAlignment);
1986 // TODO - determine if the listenToViewSelections button is needed : see bug
1988 // selectMenu.addSeparator();
1989 // selectMenu.add(listenToViewSelections);
1992 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1994 // TODO Auto-generated method stub
1998 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2000 // TODO Auto-generated method stub
2004 protected void showAllhidden_actionPerformed(ActionEvent e)
2006 // TODO Auto-generated method stub
2010 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2012 // TODO Auto-generated method stub
2016 protected void hideAllSelection_actionPerformed(ActionEvent e)
2018 // TODO Auto-generated method stub
2022 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2024 // TODO Auto-generated method stub
2028 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2030 // TODO Auto-generated method stub
2034 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2036 // TODO Auto-generated method stub
2040 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2042 // TODO Auto-generated method stub
2046 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2048 // TODO Auto-generated method stub
2052 protected void showGroupConservation_actionPerformed(ActionEvent e)
2054 // TODO Auto-generated method stub
2058 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2060 // TODO Auto-generated method stub
2064 protected void showSeqFeaturesHeight_actionPerformed(
2065 ActionEvent actionEvent)
2067 // TODO Auto-generated method stub
2071 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2073 // TODO Auto-generated method stub
2077 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2079 // TODO Auto-generated method stub
2083 protected void followHighlight_actionPerformed()
2085 // TODO Auto-generated method stub
2089 protected void showNpFeats_actionPerformed(ActionEvent e)
2091 // TODO Auto-generated method stub
2095 protected void showDbRefs_actionPerformed(ActionEvent e)
2097 // TODO Auto-generated method stub
2101 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2105 protected void showProducts_actionPerformed(ActionEvent e)
2109 protected void buildSortByAnnotationScoresMenu()
2113 protected void extractScores_actionPerformed(ActionEvent e)
2117 protected void outputText_actionPerformed(ActionEvent e)
2121 public void addFromFile_actionPerformed(ActionEvent e)
2126 public void addFromText_actionPerformed(ActionEvent e)
2131 public void addFromURL_actionPerformed(ActionEvent e)
2136 public void exportFeatures_actionPerformed(ActionEvent e)
2141 public void exportAnnotations_actionPerformed(ActionEvent e)
2146 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2150 protected void closeMenuItem_actionPerformed(boolean b)
2154 protected void redoMenuItem_actionPerformed(ActionEvent e)
2158 protected void undoMenuItem_actionPerformed(ActionEvent e)
2162 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2166 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2170 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2174 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2178 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2182 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2186 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2190 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2194 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2198 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2202 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2206 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2210 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2214 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2218 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2222 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2226 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2230 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2234 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2238 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2242 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2246 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2250 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2254 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2258 protected void clustalColour_actionPerformed(ActionEvent e)
2262 protected void zappoColour_actionPerformed(ActionEvent e)
2266 protected void taylorColour_actionPerformed(ActionEvent e)
2270 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2274 protected void helixColour_actionPerformed(ActionEvent e)
2278 protected void strandColour_actionPerformed(ActionEvent e)
2282 protected void turnColour_actionPerformed(ActionEvent e)
2286 protected void buriedColour_actionPerformed(ActionEvent e)
2290 protected void userDefinedColour_actionPerformed(ActionEvent e)
2294 protected void PIDColour_actionPerformed(ActionEvent e)
2298 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2302 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2307 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2310 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2314 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2318 protected void printMenuItem_actionPerformed(ActionEvent e)
2322 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2326 protected void findMenuItem_actionPerformed(ActionEvent e)
2330 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2334 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2338 protected void nucleotideColour_actionPerformed(ActionEvent e)
2342 protected void deleteGroups_actionPerformed(ActionEvent e)
2346 protected void createGroup_actionPerformed(ActionEvent e)
2350 protected void unGroup_actionPerformed(ActionEvent e)
2354 protected void copy_actionPerformed(ActionEvent e)
2358 protected void cut_actionPerformed(ActionEvent e)
2362 protected void delete_actionPerformed(ActionEvent e)
2366 protected void pasteNew_actionPerformed(ActionEvent e)
2370 protected void pasteThis_actionPerformed(ActionEvent e)
2374 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2378 public void createPNG(java.io.File f)
2382 protected void font_actionPerformed(ActionEvent e)
2386 protected void seqLimit_actionPerformed(ActionEvent e)
2390 public void seqDBRef_actionPerformed(ActionEvent e)
2395 public void createEPS(java.io.File f)
2399 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2405 * Template method to handle the 'load T-Coffee scores' menu event.
2407 * Subclasses override this method to provide a custom action.
2412 protected void loadScores_actionPerformed(ActionEvent event)
2418 * Template method to handle the 'Color T-Coffee scores' menu event.
2420 * Subclasses override this method to provide a custom action.
2425 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2430 protected void jpred_actionPerformed(ActionEvent e)
2434 protected void scaleAbove_actionPerformed(ActionEvent e)
2438 protected void scaleLeft_actionPerformed(ActionEvent e)
2442 protected void scaleRight_actionPerformed(ActionEvent e)
2446 protected void modifyPID_actionPerformed(ActionEvent e)
2450 protected void modifyConservation_actionPerformed(ActionEvent e)
2454 protected void saveAs_actionPerformed(ActionEvent e)
2458 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2462 public void vamsasStore_actionPerformed(ActionEvent e)
2467 public void vamsasLoad_actionPerformed(ActionEvent e)
2472 public void showTranslation_actionPerformed(ActionEvent e)
2477 public void featureSettings_actionPerformed(ActionEvent e)
2482 public void fetchSequence_actionPerformed(ActionEvent e)
2487 public void smoothFont_actionPerformed(ActionEvent e)
2492 public void annotationColour_actionPerformed(ActionEvent e)
2497 public void rnahelicesColour_actionPerformed(ActionEvent e)
2502 public void associatedData_actionPerformed(ActionEvent e)
2507 public void autoCalculate_actionPerformed(ActionEvent e)
2512 public void sortByTreeOption_actionPerformed(ActionEvent e)
2517 public void showAllSeqs_actionPerformed(ActionEvent e)
2522 public void showAllColumns_actionPerformed(ActionEvent e)
2527 public void hideSelSequences_actionPerformed(ActionEvent e)
2532 public void hideSelColumns_actionPerformed(ActionEvent e)
2537 public void hiddenMarkers_actionPerformed(ActionEvent e)
2542 public void findPdbId_actionPerformed(ActionEvent e)
2547 public void enterPdbId_actionPerformed(ActionEvent e)
2552 public void pdbFile_actionPerformed(ActionEvent e)
2557 public void invertColSel_actionPerformed(ActionEvent e)
2562 public void tabSelectionChanged(int sel)
2567 public void tabbedPane_mousePressed(MouseEvent e)
2572 public void tabbedPane_focusGained(FocusEvent e)
2577 public void save_actionPerformed(ActionEvent e)
2582 public void reload_actionPerformed(ActionEvent e)
2587 public void newView_actionPerformed(ActionEvent e)
2592 public void textColour_actionPerformed(ActionEvent e)
2597 public void idRightAlign_actionPerformed(ActionEvent e)
2602 public void expandViews_actionPerformed(ActionEvent e)
2607 public void gatherViews_actionPerformed(ActionEvent e)
2612 public void buildTreeMenu()
2617 public void pageSetup_actionPerformed(ActionEvent e)
2622 public void alignmentProperties()
2627 protected void expand_newalign(ActionEvent e)
2629 // TODO Auto-generated method stub