2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.jbgui;
22 import java.awt.event.*;
25 import javax.swing.event.*;
27 import jalview.schemes.*;
29 public class GAlignFrame extends JInternalFrame
31 protected JMenuBar alignFrameMenuBar = new JMenuBar();
33 protected JMenu fileMenu = new JMenu();
35 protected JMenuItem closeMenuItem = new JMenuItem();
37 protected JMenu editMenu = new JMenu();
39 protected JMenu viewMenu = new JMenu();
41 protected JMenu colourMenu = new JMenu();
43 protected JMenu calculateMenu = new JMenu();
45 protected JMenu webService = new JMenu();
47 protected JMenuItem webServiceNoServices;
49 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
51 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
53 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
55 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
57 protected JMenuItem remove2RightMenuItem = new JMenuItem();
59 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
61 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
63 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
65 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
67 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
69 protected JMenuItem sortIDMenuItem = new JMenuItem();
71 protected JMenuItem sortGroupMenuItem = new JMenuItem();
73 protected JMenu sortByAnnotScore = new JMenu();
75 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
77 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
79 protected JMenuItem PCAMenuItem = new JMenuItem();
81 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
83 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
85 BorderLayout borderLayout1 = new BorderLayout();
87 public JLabel statusBar = new JLabel();
89 protected JMenuItem saveAs = new JMenuItem();
91 protected JMenu outputTextboxMenu = new JMenu();
93 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
95 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
97 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
99 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
101 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
103 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
105 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
107 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
109 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
111 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
113 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
115 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
117 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
119 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
121 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
123 JMenuItem htmlMenuItem = new JMenuItem();
125 JMenuItem overviewMenuItem = new JMenuItem();
127 protected JMenuItem undoMenuItem = new JMenuItem();
129 protected JMenuItem redoMenuItem = new JMenuItem();
131 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
133 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
135 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
137 JMenuItem printMenuItem = new JMenuItem();
139 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
141 JMenuItem findMenuItem = new JMenuItem();
143 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
145 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
147 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
149 JMenuItem deleteGroups = new JMenuItem();
151 JMenuItem delete = new JMenuItem();
153 JMenuItem copy = new JMenuItem();
155 JMenuItem cut = new JMenuItem();
157 JMenu pasteMenu = new JMenu();
159 JMenuItem pasteNew = new JMenuItem();
161 JMenuItem pasteThis = new JMenuItem();
163 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
165 JMenuItem createPNG = new JMenuItem();
167 protected JMenuItem font = new JMenuItem();
169 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
171 JMenuItem epsFile = new JMenuItem();
173 JMenuItem LoadtreeMenuItem = new JMenuItem();
175 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
177 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
179 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
181 protected JMenuItem modifyPID = new JMenuItem();
183 protected JMenuItem modifyConservation = new JMenuItem();
185 protected JMenu sortByTreeMenu = new JMenu();
187 protected JMenu sort = new JMenu();
189 JMenu calculate = new JMenu();
191 JMenu jMenu2 = new JMenu();
193 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
194 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
195 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
197 protected ButtonGroup colours = new ButtonGroup();
199 JMenuItem vamsasStore = new JMenuItem();
201 protected JMenuItem showTranslation = new JMenuItem();
203 protected JMenuItem extractScores = new JMenuItem();
205 protected JMenu showProducts = new JMenu();
207 public JMenuItem featureSettings = new JMenuItem();
209 JMenuItem fetchSequence = new JMenuItem();
211 JMenuItem annotationColour = new JMenuItem();
213 JMenuItem associatedData = new JMenuItem();
215 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
217 JMenu addSequenceMenu = new JMenu();
219 JMenuItem addFromFile = new JMenuItem();
221 JMenuItem addFromText = new JMenuItem();
223 JMenuItem addFromURL = new JMenuItem();
225 JMenuItem exportAnnotations = new JMenuItem();
227 JMenuItem exportFeatures = new JMenuItem();
229 protected JPanel statusPanel = new JPanel();
231 GridLayout gridLayout1 = new GridLayout();
233 JMenu jMenu3 = new JMenu();
235 JMenuItem showAllSeqs = new JMenuItem();
237 JMenuItem showAllColumns = new JMenuItem();
239 JMenu hideMenu = new JMenu();
241 JMenuItem hideSelSequences = new JMenuItem();
243 JMenuItem hideSelColumns = new JMenuItem();
245 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
247 JMenuItem invertColSel = new JMenuItem();
249 protected JTabbedPane tabbedPane = new JTabbedPane();
251 JMenuItem save = new JMenuItem();
253 protected JMenuItem reload = new JMenuItem();
255 JMenuItem newView = new JMenuItem();
257 JMenuItem textColour = new JMenuItem();
259 JMenu formatMenu = new JMenu();
261 JMenu selectMenu = new JMenu();
263 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
265 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
267 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
269 protected JMenuItem gatherViews = new JMenuItem();
271 protected JMenuItem expandViews = new JMenuItem();
273 JMenuItem pageSetup = new JMenuItem();
275 JMenuItem alignmentProperties = new JMenuItem();
277 JMenu tooltipSettingsMenu = new JMenu();
284 setJMenuBar(alignFrameMenuBar);
286 // dynamically fill save as menu with available formats
287 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
289 JMenuItem item = new JMenuItem(
290 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
292 item.addActionListener(new java.awt.event.ActionListener()
294 public void actionPerformed(ActionEvent e)
296 outputText_actionPerformed(e);
300 outputTextboxMenu.add(item);
302 } catch (Exception e)
306 if (!new jalview.util.Platform().isAMac())
308 closeMenuItem.setMnemonic('C');
309 outputTextboxMenu.setMnemonic('T');
310 undoMenuItem.setMnemonic('Z');
311 redoMenuItem.setMnemonic('0');
312 copy.setMnemonic('C');
313 cut.setMnemonic('U');
314 pasteMenu.setMnemonic('P');
315 reload.setMnemonic('R');
318 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
320 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
321 .getUserColourSchemes().keys();
323 while (userColours.hasMoreElements())
325 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
326 userColours.nextElement().toString());
327 radioItem.setName("USER_DEFINED");
328 radioItem.addMouseListener(new MouseAdapter()
330 public void mousePressed(MouseEvent evt)
332 if (evt.isControlDown()
333 || SwingUtilities.isRightMouseButton(evt))
336 .removeActionListener(radioItem.getActionListeners()[0]);
338 int option = JOptionPane.showInternalConfirmDialog(
339 jalview.gui.Desktop.desktop,
340 "Remove from default list?",
341 "Remove user defined colour",
342 JOptionPane.YES_NO_OPTION);
343 if (option == JOptionPane.YES_OPTION)
345 jalview.gui.UserDefinedColours
346 .removeColourFromDefaults(radioItem.getText());
347 colourMenu.remove(radioItem);
351 radioItem.addActionListener(new ActionListener()
353 public void actionPerformed(ActionEvent evt)
355 userDefinedColour_actionPerformed(evt);
362 radioItem.addActionListener(new ActionListener()
364 public void actionPerformed(ActionEvent evt)
366 userDefinedColour_actionPerformed(evt);
369 colourMenu.insert(radioItem, 15);
370 colours.add(radioItem);
373 colours.add(noColourmenuItem);
374 colours.add(clustalColour);
375 colours.add(zappoColour);
376 colours.add(taylorColour);
377 colours.add(hydrophobicityColour);
378 colours.add(helixColour);
379 colours.add(strandColour);
380 colours.add(turnColour);
381 colours.add(buriedColour);
382 colours.add(userDefinedColour);
383 colours.add(PIDColour);
384 colours.add(BLOSUM62Colour);
385 colours.add(nucleotideColour);
387 setColourSelected(jalview.bin.Cache
388 .getDefault("DEFAULT_COLOUR", "None"));
392 public void setColourSelected(String defaultColour)
395 if (defaultColour != null)
397 int index = ColourSchemeProperty
398 .getColourIndexFromName(defaultColour);
402 case ColourSchemeProperty.NONE:
403 noColourmenuItem.setSelected(true);
405 case ColourSchemeProperty.CLUSTAL:
406 clustalColour.setSelected(true);
410 case ColourSchemeProperty.BLOSUM:
411 BLOSUM62Colour.setSelected(true);
415 case ColourSchemeProperty.PID:
416 PIDColour.setSelected(true);
420 case ColourSchemeProperty.ZAPPO:
421 zappoColour.setSelected(true);
425 case ColourSchemeProperty.TAYLOR:
426 taylorColour.setSelected(true);
429 case ColourSchemeProperty.HYDROPHOBIC:
430 hydrophobicityColour.setSelected(true);
434 case ColourSchemeProperty.HELIX:
435 helixColour.setSelected(true);
439 case ColourSchemeProperty.STRAND:
440 strandColour.setSelected(true);
444 case ColourSchemeProperty.TURN:
445 turnColour.setSelected(true);
449 case ColourSchemeProperty.BURIED:
450 buriedColour.setSelected(true);
454 case ColourSchemeProperty.NUCLEOTIDE:
455 nucleotideColour.setSelected(true);
459 case ColourSchemeProperty.USER_DEFINED:
460 userDefinedColour.setSelected(true);
468 private void jbInit() throws Exception
470 fileMenu.setText("File");
471 saveAs.setText("Save As...");
472 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
473 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
474 .getMenuShortcutKeyMask()
475 | java.awt.event.KeyEvent.SHIFT_MASK, false));
476 saveAs.addActionListener(new ActionListener()
478 public void actionPerformed(ActionEvent e)
480 saveAs_actionPerformed(e);
483 closeMenuItem.setText("Close");
484 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
485 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
486 .getMenuShortcutKeyMask(), false));
487 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
489 public void actionPerformed(ActionEvent e)
491 closeMenuItem_actionPerformed(false);
494 editMenu.setText("Edit");
495 viewMenu.setText("View");
496 colourMenu.setText("Colour");
497 calculateMenu.setText("Calculate");
498 webService.setText("Web Service");
499 selectAllSequenceMenuItem.setText("Select All");
500 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
501 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
502 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
503 selectAllSequenceMenuItem
504 .addActionListener(new java.awt.event.ActionListener()
506 public void actionPerformed(ActionEvent e)
508 selectAllSequenceMenuItem_actionPerformed(e);
511 deselectAllSequenceMenuItem.setText("Deselect All");
512 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
513 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
514 deselectAllSequenceMenuItem
515 .addActionListener(new java.awt.event.ActionListener()
517 public void actionPerformed(ActionEvent e)
519 deselectAllSequenceMenuItem_actionPerformed(e);
522 invertSequenceMenuItem.setText("Invert Sequence Selection");
523 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
524 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
525 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
526 invertSequenceMenuItem
527 .addActionListener(new java.awt.event.ActionListener()
529 public void actionPerformed(ActionEvent e)
531 invertSequenceMenuItem_actionPerformed(e);
534 remove2LeftMenuItem.setText("Remove Left");
535 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
536 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
537 .getMenuShortcutKeyMask(), false));
539 .addActionListener(new java.awt.event.ActionListener()
541 public void actionPerformed(ActionEvent e)
543 remove2LeftMenuItem_actionPerformed(e);
546 remove2RightMenuItem.setText("Remove Right");
547 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
548 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
549 .getMenuShortcutKeyMask(), false));
551 .addActionListener(new java.awt.event.ActionListener()
553 public void actionPerformed(ActionEvent e)
555 remove2RightMenuItem_actionPerformed(e);
558 removeGappedColumnMenuItem.setText("Remove Empty Columns");
559 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
560 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
561 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
562 removeGappedColumnMenuItem
563 .addActionListener(new java.awt.event.ActionListener()
565 public void actionPerformed(ActionEvent e)
567 removeGappedColumnMenuItem_actionPerformed(e);
570 removeAllGapsMenuItem.setText("Remove All Gaps");
571 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
572 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
573 .getDefaultToolkit().getMenuShortcutKeyMask()
574 | java.awt.event.KeyEvent.SHIFT_MASK, false));
575 removeAllGapsMenuItem
576 .addActionListener(new java.awt.event.ActionListener()
578 public void actionPerformed(ActionEvent e)
580 removeAllGapsMenuItem_actionPerformed(e);
583 viewBoxesMenuItem.setText("Boxes");
584 viewBoxesMenuItem.setState(true);
585 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
587 public void actionPerformed(ActionEvent e)
589 viewBoxesMenuItem_actionPerformed(e);
592 viewTextMenuItem.setText("Text");
593 viewTextMenuItem.setState(true);
594 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
596 public void actionPerformed(ActionEvent e)
598 viewTextMenuItem_actionPerformed(e);
601 sortPairwiseMenuItem.setText("by Pairwise Identity");
603 .addActionListener(new java.awt.event.ActionListener()
605 public void actionPerformed(ActionEvent e)
607 sortPairwiseMenuItem_actionPerformed(e);
610 sortIDMenuItem.setText("by ID");
611 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
613 public void actionPerformed(ActionEvent e)
615 sortIDMenuItem_actionPerformed(e);
618 sortGroupMenuItem.setText("by Group");
619 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
621 public void actionPerformed(ActionEvent e)
623 sortGroupMenuItem_actionPerformed(e);
626 removeRedundancyMenuItem.setText("Remove Redundancy...");
627 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
628 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
629 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
630 removeRedundancyMenuItem
631 .addActionListener(new java.awt.event.ActionListener()
633 public void actionPerformed(ActionEvent e)
635 removeRedundancyMenuItem_actionPerformed(e);
638 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
639 pairwiseAlignmentMenuItem
640 .addActionListener(new java.awt.event.ActionListener()
642 public void actionPerformed(ActionEvent e)
644 pairwiseAlignmentMenuItem_actionPerformed(e);
647 PCAMenuItem.setText("Principal Component Analysis");
648 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
650 public void actionPerformed(ActionEvent e)
652 PCAMenuItem_actionPerformed(e);
655 averageDistanceTreeMenuItem
656 .setText("Average Distance Using % Identity");
657 averageDistanceTreeMenuItem
658 .addActionListener(new java.awt.event.ActionListener()
660 public void actionPerformed(ActionEvent e)
662 averageDistanceTreeMenuItem_actionPerformed(e);
665 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
666 neighbourTreeMenuItem
667 .addActionListener(new java.awt.event.ActionListener()
669 public void actionPerformed(ActionEvent e)
671 neighbourTreeMenuItem_actionPerformed(e);
674 this.getContentPane().setLayout(borderLayout1);
675 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
676 statusBar.setBackground(Color.white);
677 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
678 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
679 statusBar.setText("Status bar");
680 outputTextboxMenu.setText("Output to Textbox");
681 clustalColour.setText("Clustalx");
683 clustalColour.addActionListener(new java.awt.event.ActionListener()
685 public void actionPerformed(ActionEvent e)
687 clustalColour_actionPerformed(e);
690 zappoColour.setText("Zappo");
691 zappoColour.addActionListener(new java.awt.event.ActionListener()
693 public void actionPerformed(ActionEvent e)
695 zappoColour_actionPerformed(e);
698 taylorColour.setText("Taylor");
699 taylorColour.addActionListener(new java.awt.event.ActionListener()
701 public void actionPerformed(ActionEvent e)
703 taylorColour_actionPerformed(e);
706 hydrophobicityColour.setText("Hydrophobicity");
708 .addActionListener(new java.awt.event.ActionListener()
710 public void actionPerformed(ActionEvent e)
712 hydrophobicityColour_actionPerformed(e);
715 helixColour.setText("Helix Propensity");
716 helixColour.addActionListener(new java.awt.event.ActionListener()
718 public void actionPerformed(ActionEvent e)
720 helixColour_actionPerformed(e);
723 strandColour.setText("Strand Propensity");
724 strandColour.addActionListener(new java.awt.event.ActionListener()
726 public void actionPerformed(ActionEvent e)
728 strandColour_actionPerformed(e);
731 turnColour.setText("Turn Propensity");
732 turnColour.addActionListener(new java.awt.event.ActionListener()
734 public void actionPerformed(ActionEvent e)
736 turnColour_actionPerformed(e);
739 buriedColour.setText("Buried Index");
740 buriedColour.addActionListener(new java.awt.event.ActionListener()
742 public void actionPerformed(ActionEvent e)
744 buriedColour_actionPerformed(e);
747 userDefinedColour.setText("User Defined...");
748 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
750 public void actionPerformed(ActionEvent e)
752 userDefinedColour_actionPerformed(e);
755 PIDColour.setText("Percentage Identity");
756 PIDColour.addActionListener(new java.awt.event.ActionListener()
758 public void actionPerformed(ActionEvent e)
760 PIDColour_actionPerformed(e);
763 BLOSUM62Colour.setText("BLOSUM62 Score");
764 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
766 public void actionPerformed(ActionEvent e)
768 BLOSUM62Colour_actionPerformed(e);
771 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
772 avDistanceTreeBlosumMenuItem
773 .addActionListener(new java.awt.event.ActionListener()
775 public void actionPerformed(ActionEvent e)
777 avTreeBlosumMenuItem_actionPerformed(e);
780 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
782 .addActionListener(new java.awt.event.ActionListener()
784 public void actionPerformed(ActionEvent e)
786 njTreeBlosumMenuItem_actionPerformed(e);
789 annotationPanelMenuItem.setActionCommand("");
790 annotationPanelMenuItem.setText("Show Annotations");
791 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
792 "SHOW_ANNOTATIONS", true));
793 annotationPanelMenuItem
794 .addActionListener(new java.awt.event.ActionListener()
796 public void actionPerformed(ActionEvent e)
798 annotationPanelMenuItem_actionPerformed(e);
801 colourTextMenuItem.setText("Colour Text");
803 .addActionListener(new java.awt.event.ActionListener()
805 public void actionPerformed(ActionEvent e)
807 colourTextMenuItem_actionPerformed(e);
810 htmlMenuItem.setText("HTML");
811 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
813 public void actionPerformed(ActionEvent e)
815 htmlMenuItem_actionPerformed(e);
818 overviewMenuItem.setText("Overview Window");
819 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
821 public void actionPerformed(ActionEvent e)
823 overviewMenuItem_actionPerformed(e);
826 undoMenuItem.setEnabled(false);
827 undoMenuItem.setText("Undo");
828 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
829 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
830 .getMenuShortcutKeyMask(), false));
831 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
833 public void actionPerformed(ActionEvent e)
835 undoMenuItem_actionPerformed(e);
838 redoMenuItem.setEnabled(false);
839 redoMenuItem.setText("Redo");
840 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
841 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
842 .getMenuShortcutKeyMask(), false));
843 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
845 public void actionPerformed(ActionEvent e)
847 redoMenuItem_actionPerformed(e);
850 conservationMenuItem.setText("By Conservation");
852 .addActionListener(new java.awt.event.ActionListener()
854 public void actionPerformed(ActionEvent e)
856 conservationMenuItem_actionPerformed(e);
859 noColourmenuItem.setText("None");
860 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
862 public void actionPerformed(ActionEvent e)
864 noColourmenuItem_actionPerformed(e);
867 wrapMenuItem.setText("Wrap");
868 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
870 public void actionPerformed(ActionEvent e)
872 wrapMenuItem_actionPerformed(e);
875 printMenuItem.setText("Print ...");
876 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
877 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
878 .getMenuShortcutKeyMask(), false));
879 printMenuItem.addActionListener(new java.awt.event.ActionListener()
881 public void actionPerformed(ActionEvent e)
883 printMenuItem_actionPerformed(e);
886 renderGapsMenuItem.setText("Show Gaps");
887 renderGapsMenuItem.setState(true);
889 .addActionListener(new java.awt.event.ActionListener()
891 public void actionPerformed(ActionEvent e)
893 renderGapsMenuItem_actionPerformed(e);
896 findMenuItem.setText("Find...");
897 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
898 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
899 .getMenuShortcutKeyMask(), false));
900 findMenuItem.addActionListener(new java.awt.event.ActionListener()
902 public void actionPerformed(ActionEvent e)
904 findMenuItem_actionPerformed(e);
907 abovePIDThreshold.setText("Above Identity Threshold");
908 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
910 public void actionPerformed(ActionEvent e)
912 abovePIDThreshold_actionPerformed(e);
915 showSeqFeatures.setText("Show Sequence Features");
916 showSeqFeatures.addActionListener(new ActionListener()
918 public void actionPerformed(ActionEvent actionEvent)
920 showSeqFeatures_actionPerformed(actionEvent);
923 showDbRefsMenuitem.setText("Show Database Refs");
924 showDbRefsMenuitem.addActionListener(new ActionListener()
927 public void actionPerformed(ActionEvent e)
929 showDbRefs_actionPerformed(e);
933 showNpFeatsMenuitem.setText("Show Non-Positional Features");
934 showNpFeatsMenuitem.addActionListener(new ActionListener()
937 public void actionPerformed(ActionEvent e)
939 showNpFeats_actionPerformed(e);
943 nucleotideColour.setText("Nucleotide");
944 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
946 public void actionPerformed(ActionEvent e)
948 nucleotideColour_actionPerformed(e);
951 deleteGroups.setText("Undefine groups");
952 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
953 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
954 .getMenuShortcutKeyMask(), false));
955 deleteGroups.addActionListener(new java.awt.event.ActionListener()
957 public void actionPerformed(ActionEvent e)
959 deleteGroups_actionPerformed(e);
962 copy.setText("Copy");
963 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
964 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
965 .getMenuShortcutKeyMask(), false));
967 copy.addActionListener(new java.awt.event.ActionListener()
969 public void actionPerformed(ActionEvent e)
971 copy_actionPerformed(e);
975 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
976 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
977 .getMenuShortcutKeyMask(), false));
978 cut.addActionListener(new java.awt.event.ActionListener()
980 public void actionPerformed(ActionEvent e)
982 cut_actionPerformed(e);
985 delete.setText("Delete");
986 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
987 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
988 delete.addActionListener(new java.awt.event.ActionListener()
990 public void actionPerformed(ActionEvent e)
992 delete_actionPerformed(e);
995 pasteMenu.setText("Paste");
996 pasteNew.setText("To New Alignment");
997 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
998 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
999 .getMenuShortcutKeyMask()
1000 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1001 pasteNew.addActionListener(new java.awt.event.ActionListener()
1003 public void actionPerformed(ActionEvent e)
1005 pasteNew_actionPerformed(e);
1008 pasteThis.setText("Add To This Alignment");
1009 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1010 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1011 .getMenuShortcutKeyMask(), false));
1012 pasteThis.addActionListener(new java.awt.event.ActionListener()
1014 public void actionPerformed(ActionEvent e)
1016 pasteThis_actionPerformed(e);
1019 applyToAllGroups.setText("Apply Colour To All Groups");
1020 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1022 public void actionPerformed(ActionEvent e)
1024 applyToAllGroups_actionPerformed(e);
1027 createPNG.addActionListener(new java.awt.event.ActionListener()
1029 public void actionPerformed(ActionEvent e)
1034 createPNG.setActionCommand("Save As PNG Image");
1035 createPNG.setText("PNG");
1036 font.setText("Font...");
1037 font.addActionListener(new java.awt.event.ActionListener()
1039 public void actionPerformed(ActionEvent e)
1041 font_actionPerformed(e);
1045 seqLimits.setText("Show Sequence Limits");
1046 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1047 seqLimits.addActionListener(new java.awt.event.ActionListener()
1049 public void actionPerformed(ActionEvent e)
1051 seqLimit_actionPerformed(e);
1054 epsFile.setText("EPS");
1055 epsFile.addActionListener(new java.awt.event.ActionListener()
1057 public void actionPerformed(ActionEvent e)
1062 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1063 LoadtreeMenuItem.setText("Load Associated Tree");
1064 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1066 public void actionPerformed(ActionEvent e)
1068 LoadtreeMenuItem_actionPerformed(e);
1071 scaleAbove.setVisible(false);
1072 scaleAbove.setText("Scale Above");
1073 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1075 public void actionPerformed(ActionEvent e)
1077 scaleAbove_actionPerformed(e);
1080 scaleLeft.setVisible(false);
1081 scaleLeft.setSelected(true);
1082 scaleLeft.setText("Scale Left");
1083 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1085 public void actionPerformed(ActionEvent e)
1087 scaleLeft_actionPerformed(e);
1090 scaleRight.setVisible(false);
1091 scaleRight.setSelected(true);
1092 scaleRight.setText("Scale Right");
1093 scaleRight.addActionListener(new java.awt.event.ActionListener()
1095 public void actionPerformed(ActionEvent e)
1097 scaleRight_actionPerformed(e);
1100 centreColumnLabelsMenuItem.setVisible(true);
1101 centreColumnLabelsMenuItem.setState(false);
1102 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1103 centreColumnLabelsMenuItem
1104 .addActionListener(new java.awt.event.ActionListener()
1106 public void actionPerformed(ActionEvent e)
1108 centreColumnLabels_actionPerformed(e);
1111 followHighlightMenuItem.setVisible(true);
1112 followHighlightMenuItem.setState(true);
1113 followHighlightMenuItem.setText("Automatic Scrolling");
1114 followHighlightMenuItem.addActionListener(new ActionListener()
1117 public void actionPerformed(ActionEvent e)
1119 followHighlight_actionPerformed();
1124 modifyPID.setText("Modify Identity Threshold...");
1125 modifyPID.addActionListener(new java.awt.event.ActionListener()
1127 public void actionPerformed(ActionEvent e)
1129 modifyPID_actionPerformed(e);
1132 modifyConservation.setText("Modify Conservation Threshold...");
1134 .addActionListener(new java.awt.event.ActionListener()
1136 public void actionPerformed(ActionEvent e)
1138 modifyConservation_actionPerformed(e);
1141 sortByTreeMenu.setText("By Tree Order");
1142 sort.setText("Sort");
1143 sort.addMenuListener(new MenuListener()
1145 public void menuSelected(MenuEvent e)
1150 public void menuDeselected(MenuEvent e)
1154 public void menuCanceled(MenuEvent e)
1158 sortByAnnotScore.setText("by Score");
1159 sort.add(sortByAnnotScore);
1160 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1163 public void menuCanceled(MenuEvent e)
1167 public void menuDeselected(MenuEvent e)
1171 public void menuSelected(MenuEvent e)
1173 buildSortByAnnotationScoresMenu();
1176 sortByAnnotScore.setVisible(false);
1178 calculate.setText("Calculate Tree");
1180 jMenu2.setText("Export Image");
1181 padGapsMenuitem.setText("Pad Gaps");
1182 padGapsMenuitem.setState(jalview.bin.Cache
1183 .getDefault("PAD_GAPS", false));
1184 padGapsMenuitem.addActionListener(new ActionListener()
1186 public void actionPerformed(ActionEvent e)
1188 padGapsMenuitem_actionPerformed(e);
1191 vamsasStore.setVisible(false);
1192 vamsasStore.setText("VAMSAS store");
1193 vamsasStore.addActionListener(new ActionListener()
1195 public void actionPerformed(ActionEvent e)
1197 vamsasStore_actionPerformed(e);
1200 showTranslation.setText("Translate cDNA");
1201 showTranslation.addActionListener(new ActionListener()
1203 public void actionPerformed(ActionEvent e)
1205 showTranslation_actionPerformed(e);
1208 extractScores.setText("Extract Scores...");
1209 extractScores.addActionListener(new ActionListener()
1211 public void actionPerformed(ActionEvent e)
1213 extractScores_actionPerformed(e);
1216 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1218 showProducts.setText("Get Cross References");
1220 * showProducts.addActionListener(new ActionListener() {
1222 * public void actionPerformed(ActionEvent e) {
1223 * showProducts_actionPerformed(e); } });
1225 featureSettings.setText("Feature Settings...");
1226 featureSettings.addActionListener(new ActionListener()
1228 public void actionPerformed(ActionEvent e)
1230 featureSettings_actionPerformed(e);
1233 fetchSequence.setText("Fetch Sequence(s)...");
1234 fetchSequence.addActionListener(new ActionListener()
1236 public void actionPerformed(ActionEvent e)
1238 fetchSequence_actionPerformed(e);
1242 annotationColour.setText("By Annotation...");
1243 annotationColour.addActionListener(new ActionListener()
1245 public void actionPerformed(ActionEvent e)
1247 annotationColour_actionPerformed(e);
1250 associatedData.setText("Load Features / Annotations");
1251 associatedData.addActionListener(new ActionListener()
1253 public void actionPerformed(ActionEvent e)
1255 associatedData_actionPerformed(e);
1258 autoCalculate.setText("Autocalculate Consensus");
1259 autoCalculate.setState(jalview.bin.Cache.getDefault(
1260 "AUTO_CALC_CONSENSUS", true));
1261 autoCalculate.addActionListener(new ActionListener()
1263 public void actionPerformed(ActionEvent e)
1265 autoCalculate_actionPerformed(e);
1268 addSequenceMenu.setText("Add Sequences");
1269 addFromFile.setText("From File");
1270 addFromFile.addActionListener(new ActionListener()
1272 public void actionPerformed(ActionEvent e)
1274 addFromFile_actionPerformed(e);
1277 addFromText.setText("From Textbox");
1278 addFromText.addActionListener(new ActionListener()
1280 public void actionPerformed(ActionEvent e)
1282 addFromText_actionPerformed(e);
1285 addFromURL.setText("From URL");
1286 addFromURL.addActionListener(new ActionListener()
1288 public void actionPerformed(ActionEvent e)
1290 addFromURL_actionPerformed(e);
1293 exportFeatures.setText("Export Features...");
1294 exportFeatures.addActionListener(new ActionListener()
1296 public void actionPerformed(ActionEvent e)
1298 exportFeatures_actionPerformed(e);
1301 exportAnnotations.setText("Export Annotations...");
1302 exportAnnotations.addActionListener(new ActionListener()
1304 public void actionPerformed(ActionEvent e)
1306 exportAnnotations_actionPerformed(e);
1309 statusPanel.setLayout(gridLayout1);
1310 jMenu3.setText("Show");
1311 showAllSeqs.setText("All Sequences");
1312 showAllSeqs.addActionListener(new ActionListener()
1314 public void actionPerformed(ActionEvent e)
1316 showAllSeqs_actionPerformed(e);
1319 showAllColumns.setText("All Columns");
1320 showAllColumns.addActionListener(new ActionListener()
1322 public void actionPerformed(ActionEvent e)
1324 showAllColumns_actionPerformed(e);
1327 hideMenu.setText("Hide");
1328 hideSelSequences.setText("Selected Sequences");
1329 hideSelSequences.addActionListener(new ActionListener()
1331 public void actionPerformed(ActionEvent e)
1333 hideSelSequences_actionPerformed(e);
1336 hideSelColumns.setText("Selected Columns");
1337 hideSelColumns.addActionListener(new ActionListener()
1339 public void actionPerformed(ActionEvent e)
1341 hideSelColumns_actionPerformed(e);
1344 hiddenMarkers.setText("Show Hidden Markers");
1345 hiddenMarkers.addActionListener(new ActionListener()
1347 public void actionPerformed(ActionEvent e)
1349 hiddenMarkers_actionPerformed(e);
1352 invertColSel.setText("Invert Column Selection");
1353 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1354 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1355 .getMenuShortcutKeyMask()
1356 | java.awt.event.KeyEvent.ALT_MASK, false));
1357 invertColSel.addActionListener(new ActionListener()
1359 public void actionPerformed(ActionEvent e)
1361 invertColSel_actionPerformed(e);
1364 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1366 public void stateChanged(ChangeEvent evt)
1368 JTabbedPane pane = (JTabbedPane) evt.getSource();
1369 int sel = pane.getSelectedIndex();
1370 tabSelectionChanged(sel);
1373 tabbedPane.addMouseListener(new MouseAdapter()
1375 public void mousePressed(MouseEvent e)
1377 tabbedPane_mousePressed(e);
1380 tabbedPane.addFocusListener(new FocusAdapter()
1382 public void focusGained(FocusEvent e)
1384 tabbedPane_focusGained(e);
1387 save.setText("Save");
1388 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1389 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1390 .getMenuShortcutKeyMask(), false));
1391 save.addActionListener(new ActionListener()
1393 public void actionPerformed(ActionEvent e)
1395 save_actionPerformed(e);
1398 reload.setEnabled(false);
1399 reload.setText("Reload");
1400 reload.addActionListener(new ActionListener()
1402 public void actionPerformed(ActionEvent e)
1404 reload_actionPerformed(e);
1407 newView.setText("New View");
1408 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1409 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1410 .getMenuShortcutKeyMask(), false));
1411 newView.addActionListener(new ActionListener()
1413 public void actionPerformed(ActionEvent e)
1415 newView_actionPerformed(e);
1418 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1419 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1420 textColour.setText("Colour Text ...");
1421 textColour.addActionListener(new ActionListener()
1423 public void actionPerformed(ActionEvent e)
1425 textColour_actionPerformed(e);
1428 formatMenu.setText("Format");
1429 selectMenu.setText("Select");
1430 idRightAlign.setText("Right Align Sequence Id");
1431 idRightAlign.addActionListener(new ActionListener()
1433 public void actionPerformed(ActionEvent e)
1435 idRightAlign_actionPerformed(e);
1438 gatherViews.setEnabled(false);
1439 gatherViews.setText("Gather Views");
1440 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1441 java.awt.event.KeyEvent.VK_G, 0, false));
1442 gatherViews.addActionListener(new ActionListener()
1444 public void actionPerformed(ActionEvent e)
1446 gatherViews_actionPerformed(e);
1449 expandViews.setEnabled(false);
1450 expandViews.setText("Expand Views");
1451 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1452 java.awt.event.KeyEvent.VK_X, 0, false));
1453 expandViews.addActionListener(new ActionListener()
1455 public void actionPerformed(ActionEvent e)
1457 expandViews_actionPerformed(e);
1460 pageSetup.setText("Page Setup ...");
1461 pageSetup.addActionListener(new ActionListener()
1463 public void actionPerformed(ActionEvent e)
1465 pageSetup_actionPerformed(e);
1468 alignmentProperties.setText("Alignment Properties...");
1469 alignmentProperties.addActionListener(new ActionListener()
1471 public void actionPerformed(ActionEvent actionEvent)
1473 alignmentProperties();
1476 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1477 alignFrameMenuBar.add(fileMenu);
1478 alignFrameMenuBar.add(editMenu);
1479 alignFrameMenuBar.add(selectMenu);
1480 alignFrameMenuBar.add(viewMenu);
1481 alignFrameMenuBar.add(formatMenu);
1482 alignFrameMenuBar.add(colourMenu);
1483 alignFrameMenuBar.add(calculateMenu);
1484 alignFrameMenuBar.add(webService);
1485 fileMenu.add(fetchSequence);
1486 fileMenu.add(addSequenceMenu);
1487 fileMenu.add(reload);
1488 fileMenu.addSeparator();
1489 fileMenu.add(vamsasStore);
1491 fileMenu.add(saveAs);
1492 fileMenu.add(outputTextboxMenu);
1493 fileMenu.add(pageSetup);
1494 fileMenu.add(printMenuItem);
1495 fileMenu.addSeparator();
1496 fileMenu.add(jMenu2);
1497 fileMenu.add(exportFeatures);
1498 fileMenu.add(exportAnnotations);
1499 fileMenu.add(LoadtreeMenuItem);
1500 fileMenu.add(associatedData);
1501 fileMenu.addSeparator();
1502 fileMenu.add(closeMenuItem);
1503 editMenu.add(undoMenuItem);
1504 editMenu.add(redoMenuItem);
1507 editMenu.add(pasteMenu);
1508 editMenu.add(delete);
1509 editMenu.addSeparator();
1510 editMenu.add(remove2LeftMenuItem);
1511 editMenu.add(remove2RightMenuItem);
1512 editMenu.add(removeGappedColumnMenuItem);
1513 editMenu.add(removeAllGapsMenuItem);
1514 editMenu.add(removeRedundancyMenuItem);
1515 editMenu.addSeparator();
1516 editMenu.add(padGapsMenuitem);
1517 viewMenu.add(newView);
1518 viewMenu.add(expandViews);
1519 viewMenu.add(gatherViews);
1520 viewMenu.addSeparator();
1521 viewMenu.add(jMenu3);
1522 viewMenu.add(hideMenu);
1523 viewMenu.addSeparator();
1524 viewMenu.add(followHighlightMenuItem);
1525 viewMenu.add(annotationPanelMenuItem);
1526 viewMenu.addSeparator();
1527 viewMenu.add(showSeqFeatures);
1528 viewMenu.add(featureSettings);
1529 tooltipSettingsMenu.add(showDbRefsMenuitem);
1530 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1531 viewMenu.add(tooltipSettingsMenu);
1532 viewMenu.addSeparator();
1533 viewMenu.add(alignmentProperties);
1534 viewMenu.addSeparator();
1535 viewMenu.add(overviewMenuItem);
1536 colourMenu.add(applyToAllGroups);
1537 colourMenu.add(textColour);
1538 colourMenu.addSeparator();
1539 colourMenu.add(noColourmenuItem);
1540 colourMenu.add(clustalColour);
1541 colourMenu.add(BLOSUM62Colour);
1542 colourMenu.add(PIDColour);
1543 colourMenu.add(zappoColour);
1544 colourMenu.add(taylorColour);
1545 colourMenu.add(hydrophobicityColour);
1546 colourMenu.add(helixColour);
1547 colourMenu.add(strandColour);
1548 colourMenu.add(turnColour);
1549 colourMenu.add(buriedColour);
1550 colourMenu.add(nucleotideColour);
1551 colourMenu.add(userDefinedColour);
1552 colourMenu.addSeparator();
1553 colourMenu.add(conservationMenuItem);
1554 colourMenu.add(modifyConservation);
1555 colourMenu.add(abovePIDThreshold);
1556 colourMenu.add(modifyPID);
1557 colourMenu.add(annotationColour);
1558 calculateMenu.add(sort);
1559 calculateMenu.add(calculate);
1560 calculateMenu.addSeparator();
1561 calculateMenu.add(pairwiseAlignmentMenuItem);
1562 calculateMenu.add(PCAMenuItem);
1563 calculateMenu.addSeparator();
1564 calculateMenu.add(showTranslation);
1565 calculateMenu.add(showProducts);
1566 calculateMenu.add(autoCalculate);
1567 calculateMenu.addSeparator();
1568 calculateMenu.add(extractScores);
1569 webServiceNoServices = new JMenuItem("<No Services>");
1570 webService.add(webServiceNoServices);
1571 pasteMenu.add(pasteNew);
1572 pasteMenu.add(pasteThis);
1573 sort.add(sortIDMenuItem);
1574 sort.add(sortGroupMenuItem);
1575 sort.add(sortPairwiseMenuItem);
1576 sort.add(sortByTreeMenu);
1577 calculate.add(averageDistanceTreeMenuItem);
1578 calculate.add(neighbourTreeMenuItem);
1579 calculate.add(avDistanceTreeBlosumMenuItem);
1580 calculate.add(njTreeBlosumMenuItem);
1581 jMenu2.add(htmlMenuItem);
1582 jMenu2.add(epsFile);
1583 jMenu2.add(createPNG);
1584 addSequenceMenu.add(addFromFile);
1585 addSequenceMenu.add(addFromText);
1586 addSequenceMenu.add(addFromURL);
1587 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1588 statusPanel.add(statusBar, null);
1589 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1590 jMenu3.add(showAllColumns);
1591 jMenu3.add(showAllSeqs);
1592 hideMenu.add(hideSelColumns);
1593 hideMenu.add(hideSelSequences);
1594 formatMenu.add(font);
1595 formatMenu.addSeparator();
1596 formatMenu.add(wrapMenuItem);
1597 formatMenu.add(scaleAbove);
1598 formatMenu.add(scaleLeft);
1599 formatMenu.add(scaleRight);
1600 formatMenu.add(seqLimits);
1601 formatMenu.add(idRightAlign);
1602 formatMenu.add(hiddenMarkers);
1603 formatMenu.add(viewBoxesMenuItem);
1604 formatMenu.add(viewTextMenuItem);
1605 formatMenu.add(colourTextMenuItem);
1606 formatMenu.add(renderGapsMenuItem);
1607 formatMenu.add(centreColumnLabelsMenuItem);
1608 selectMenu.add(findMenuItem);
1609 selectMenu.addSeparator();
1610 selectMenu.add(selectAllSequenceMenuItem);
1611 selectMenu.add(deselectAllSequenceMenuItem);
1612 selectMenu.add(invertSequenceMenuItem);
1613 selectMenu.add(invertColSel);
1614 selectMenu.add(deleteGroups);
1617 protected void followHighlight_actionPerformed()
1619 // TODO Auto-generated method stub
1623 protected void showNpFeats_actionPerformed(ActionEvent e)
1625 // TODO Auto-generated method stub
1629 protected void showDbRefs_actionPerformed(ActionEvent e)
1631 // TODO Auto-generated method stub
1635 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1639 protected void showProducts_actionPerformed(ActionEvent e)
1643 protected void buildSortByAnnotationScoresMenu()
1647 protected void extractScores_actionPerformed(ActionEvent e)
1651 protected void outputText_actionPerformed(ActionEvent e)
1655 public void addFromFile_actionPerformed(ActionEvent e)
1660 public void addFromText_actionPerformed(ActionEvent e)
1665 public void addFromURL_actionPerformed(ActionEvent e)
1670 public void exportFeatures_actionPerformed(ActionEvent e)
1675 public void exportAnnotations_actionPerformed(ActionEvent e)
1680 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1684 protected void closeMenuItem_actionPerformed(boolean b)
1688 protected void redoMenuItem_actionPerformed(ActionEvent e)
1692 protected void undoMenuItem_actionPerformed(ActionEvent e)
1696 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1700 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1704 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1708 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1712 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1716 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1720 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1724 protected void wrapMenuItem_actionPerformed(ActionEvent e)
1728 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1732 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1736 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1740 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1744 protected void overviewMenuItem_actionPerformed(ActionEvent e)
1748 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1752 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1756 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1760 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1764 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1768 protected void PCAMenuItem_actionPerformed(ActionEvent e)
1772 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1776 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1780 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1784 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1788 protected void clustalColour_actionPerformed(ActionEvent e)
1792 protected void zappoColour_actionPerformed(ActionEvent e)
1796 protected void taylorColour_actionPerformed(ActionEvent e)
1800 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1804 protected void helixColour_actionPerformed(ActionEvent e)
1808 protected void strandColour_actionPerformed(ActionEvent e)
1812 protected void turnColour_actionPerformed(ActionEvent e)
1816 protected void buriedColour_actionPerformed(ActionEvent e)
1820 protected void userDefinedColour_actionPerformed(ActionEvent e)
1824 protected void PIDColour_actionPerformed(ActionEvent e)
1828 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1832 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1836 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1840 protected void printMenuItem_actionPerformed(ActionEvent e)
1844 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1848 protected void findMenuItem_actionPerformed(ActionEvent e)
1852 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1856 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
1860 protected void nucleotideColour_actionPerformed(ActionEvent e)
1864 protected void deleteGroups_actionPerformed(ActionEvent e)
1868 protected void copy_actionPerformed(ActionEvent e)
1872 protected void cut_actionPerformed(ActionEvent e)
1876 protected void delete_actionPerformed(ActionEvent e)
1880 protected void pasteNew_actionPerformed(ActionEvent e)
1884 protected void pasteThis_actionPerformed(ActionEvent e)
1888 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1892 public void createPNG(java.io.File f)
1896 protected void font_actionPerformed(ActionEvent e)
1900 protected void seqLimit_actionPerformed(ActionEvent e)
1904 public void seqDBRef_actionPerformed(ActionEvent e)
1909 public void createEPS(java.io.File f)
1913 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
1917 protected void jpred_actionPerformed(ActionEvent e)
1921 protected void scaleAbove_actionPerformed(ActionEvent e)
1925 protected void scaleLeft_actionPerformed(ActionEvent e)
1929 protected void scaleRight_actionPerformed(ActionEvent e)
1933 protected void modifyPID_actionPerformed(ActionEvent e)
1937 protected void modifyConservation_actionPerformed(ActionEvent e)
1941 protected void saveAs_actionPerformed(ActionEvent e)
1945 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
1949 public void vamsasStore_actionPerformed(ActionEvent e)
1954 public void vamsasLoad_actionPerformed(ActionEvent e)
1959 public void showTranslation_actionPerformed(ActionEvent e)
1964 public void featureSettings_actionPerformed(ActionEvent e)
1969 public void fetchSequence_actionPerformed(ActionEvent e)
1974 public void smoothFont_actionPerformed(ActionEvent e)
1979 public void annotationColour_actionPerformed(ActionEvent e)
1984 public void associatedData_actionPerformed(ActionEvent e)
1989 public void autoCalculate_actionPerformed(ActionEvent e)
1994 public void showAllSeqs_actionPerformed(ActionEvent e)
1999 public void showAllColumns_actionPerformed(ActionEvent e)
2004 public void hideSelSequences_actionPerformed(ActionEvent e)
2009 public void hideSelColumns_actionPerformed(ActionEvent e)
2014 public void hiddenMarkers_actionPerformed(ActionEvent e)
2019 public void findPdbId_actionPerformed(ActionEvent e)
2024 public void enterPdbId_actionPerformed(ActionEvent e)
2029 public void pdbFile_actionPerformed(ActionEvent e)
2034 public void invertColSel_actionPerformed(ActionEvent e)
2039 public void tabSelectionChanged(int sel)
2044 public void tabbedPane_mousePressed(MouseEvent e)
2049 public void tabbedPane_focusGained(FocusEvent e)
2054 public void save_actionPerformed(ActionEvent e)
2059 public void reload_actionPerformed(ActionEvent e)
2064 public void newView_actionPerformed(ActionEvent e)
2069 public void textColour_actionPerformed(ActionEvent e)
2074 public void idRightAlign_actionPerformed(ActionEvent e)
2079 public void expandViews_actionPerformed(ActionEvent e)
2084 public void gatherViews_actionPerformed(ActionEvent e)
2089 public void buildTreeMenu()
2094 public void pageSetup_actionPerformed(ActionEvent e)
2099 public void alignmentProperties()