2 * 2004 Jalview Reengineered
12 import java.awt.event.*;
15 public class GAlignFrame extends JInternalFrame
17 protected JMenuBar alignFrameMenuBar = new JMenuBar();
18 protected JMenu fileMenu = new JMenu();
19 protected JMenuItem closeMenuItem = new JMenuItem();
20 protected JMenu editMenu = new JMenu();
21 protected JMenu viewMenu = new JMenu();
22 protected JMenu colourMenu = new JMenu();
23 protected JMenu calculateMenu = new JMenu();
24 protected JMenu alignMenu = new JMenu();
25 protected JMenuItem groupsMenuItem = new JMenuItem();
26 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
27 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
28 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
29 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
30 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
31 protected JMenuItem remove2RightMenuItem = new JMenuItem();
32 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
33 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
34 protected JMenuItem setGapCharMenuItem = new JMenuItem();
35 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
36 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
37 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
38 protected JMenuItem sortIDMenuItem = new JMenuItem();
39 protected JMenuItem sortGroupMenuItem = new JMenuItem();
40 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
41 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
42 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
43 protected JMenuItem PCAMenuItem = new JMenuItem();
44 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
45 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
46 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
47 BorderLayout borderLayout1 = new BorderLayout();
48 public JLabel statusBar = new JLabel();
49 protected JMenu saveAlignmentMenu = new JMenu();
50 protected JMenu outputTextboxMenu = new JMenu();
51 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
52 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
53 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
54 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
55 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
56 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
57 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
58 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
59 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
60 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
61 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
62 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
63 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
64 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
65 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
66 JMenuItem htmlMenuItem = new JMenuItem();
67 JMenuItem overviewMenuItem = new JMenuItem();
68 protected JMenuItem undoMenuItem = new JMenuItem();
69 protected JMenuItem redoMenuItem = new JMenuItem();
70 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
71 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
72 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
73 JMenuItem printMenuItem = new JMenuItem();
74 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
75 JMenuItem findMenuItem = new JMenuItem();
76 JMenu searchMenu = new JMenu();
77 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
78 protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
79 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
80 JMenuItem deleteGroups = new JMenuItem();
81 JMenuItem delete = new JMenuItem();
82 JMenuItem copy = new JMenuItem();
83 JMenuItem cut = new JMenuItem();
84 JMenu jMenu1 = new JMenu();
85 JMenuItem pasteNew = new JMenuItem();
86 JMenuItem pasteThis = new JMenuItem();
87 protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
88 JMenuItem createPNG = new JMenuItem();
89 protected JMenuItem font = new JMenuItem();
90 protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
91 JMenuItem epsFile = new JMenuItem();
92 JMenuItem LoadtreeMenuItem = new JMenuItem();
100 setJMenuBar(alignFrameMenuBar);
103 // dynamically fill save as menu with available formats
104 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
105 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
106 saveAlignmentMenu.add( item );
107 item.addActionListener(new java.awt.event.ActionListener()
109 public void actionPerformed(ActionEvent e)
111 saveAs_actionPerformed(e);
115 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
116 item.addActionListener(new java.awt.event.ActionListener()
118 public void actionPerformed(ActionEvent e)
120 outputText_actionPerformed(e);
124 outputTextboxMenu.add( item );
133 ButtonGroup colours = new ButtonGroup();
134 colours.add(noColourmenuItem);
135 colours.add(clustalColour);
136 colours.add(zappoColour);
137 colours.add(taylorColour);
138 colours.add(hydrophobicityColour);
139 colours.add(helixColour);
140 colours.add(strandColour);
141 colours.add(turnColour);
142 colours.add(buriedColour);
143 colours.add(userDefinedColour);
144 colours.add(PIDColour);
145 colours.add(BLOSUM62Colour);
146 colours.add(nucleotideColour);
148 private void jbInit() throws Exception
150 fileMenu.setMnemonic('F');
151 fileMenu.setText("File");
152 saveAlignmentMenu.setMnemonic('L');
153 saveAlignmentMenu.setText("Save alignment to local file");
154 closeMenuItem.setMnemonic('C');
155 closeMenuItem.setText("Close");
156 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
158 public void actionPerformed(ActionEvent e)
160 closeMenuItem_actionPerformed(e);
163 editMenu.setText("Edit");
164 viewMenu.setText("View");
165 colourMenu.setText("Colour");
166 calculateMenu.setText("Calculate");
167 alignMenu.setText("Web Service");
168 groupsMenuItem.setVisible(false);
169 groupsMenuItem.setText("Groups");
170 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
172 public void actionPerformed(ActionEvent e)
174 groupsMenuItem_actionPerformed(e);
177 selectAllSequenceMenuItem.setText("Select all");
178 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
180 public void actionPerformed(ActionEvent e)
182 selectAllSequenceMenuItem_actionPerformed(e);
185 deselectAllSequenceMenuItem.setText("Clear selection");
186 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
188 public void actionPerformed(ActionEvent e)
190 deselectAllSequenceMenuItem_actionPerformed(e);
193 invertSequenceMenuItem.setText("Invert sequence selection");
194 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
196 public void actionPerformed(ActionEvent e)
198 invertSequenceMenuItem_actionPerformed(e);
201 deselectAllColumnsMenuItem.setText("Deselect all columns");
202 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
204 public void actionPerformed(ActionEvent e)
206 deselectAllColumnsMenuItem_actionPerformed(e);
209 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
210 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
212 public void actionPerformed(ActionEvent e)
214 remove2LeftMenuItem_actionPerformed(e);
217 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
218 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
220 public void actionPerformed(ActionEvent e)
222 remove2RightMenuItem_actionPerformed(e);
225 removeGappedColumnMenuItem.setText("Remove gapped columns");
226 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
228 public void actionPerformed(ActionEvent e)
230 removeGappedColumnMenuItem_actionPerformed(e);
233 removeAllGapsMenuItem.setText("Remove all gaps");
234 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
236 public void actionPerformed(ActionEvent e)
238 removeAllGapsMenuItem_actionPerformed(e);
241 setGapCharMenuItem.setText("Set gap character to \".\"");
242 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
244 public void actionPerformed(ActionEvent e)
246 setGapCharMenuItem_actionPerformed(e);
249 viewBoxesMenuItem.setText("Boxes");
250 viewBoxesMenuItem.setState(true);
251 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
253 public void actionPerformed(ActionEvent e)
255 viewBoxesMenuItem_actionPerformed(e);
258 viewTextMenuItem.setText("Text");
259 viewTextMenuItem.setState(true);
260 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
262 public void actionPerformed(ActionEvent e)
264 viewTextMenuItem_actionPerformed(e);
267 sortPairwiseMenuItem.setText("Sort by pairwise identity");
268 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
270 public void actionPerformed(ActionEvent e)
272 sortPairwiseMenuItem_actionPerformed(e);
275 sortIDMenuItem.setText("Sort by ID");
276 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
278 public void actionPerformed(ActionEvent e)
280 sortIDMenuItem_actionPerformed(e);
283 sortGroupMenuItem.setText("Sort by group");
284 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
286 public void actionPerformed(ActionEvent e)
288 sortGroupMenuItem_actionPerformed(e);
291 sortTreeOrderMenuItem.setText("Sort by tree order");
292 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
294 public void actionPerformed(ActionEvent e)
296 sortTreeOrderMenuItem_actionPerformed(e);
299 removeRedundancyMenuItem.setText("Remove redundancy");
300 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
302 public void actionPerformed(ActionEvent e)
304 removeRedundancyMenuItem_actionPerformed(e);
307 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
308 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
310 public void actionPerformed(ActionEvent e)
312 pairwiseAlignmentMenuItem_actionPerformed(e);
315 PCAMenuItem.setText("Principal component analysis");
316 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
318 public void actionPerformed(ActionEvent e)
320 PCAMenuItem_actionPerformed(e);
323 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
324 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
326 public void actionPerformed(ActionEvent e)
328 averageDistanceTreeMenuItem_actionPerformed(e);
331 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
332 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
334 public void actionPerformed(ActionEvent e)
336 neighbourTreeMenuItem_actionPerformed(e);
339 clustalAlignMenuItem.setText("Clustal alignment");
340 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
342 public void actionPerformed(ActionEvent e)
344 clustalAlignMenuItem_actionPerformed(e);
347 this.getContentPane().setLayout(borderLayout1);
348 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
349 statusBar.setBackground(Color.white);
350 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
351 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
352 statusBar.setText("Status bar");
353 outputTextboxMenu.setMnemonic('T');
354 outputTextboxMenu.setText("Output alignment via textbox");
355 clustalColour.setSelected(false);
356 clustalColour.setText("Clustalx colours");
357 clustalColour.addActionListener(new java.awt.event.ActionListener()
359 public void actionPerformed(ActionEvent e)
361 clustalColour_actionPerformed(e);
364 zappoColour.setText("Zappo colour scheme");
365 zappoColour.addActionListener(new java.awt.event.ActionListener()
367 public void actionPerformed(ActionEvent e)
369 zappoColour_actionPerformed(e);
372 taylorColour.setText("Taylor colour scheme");
373 taylorColour.addActionListener(new java.awt.event.ActionListener()
375 public void actionPerformed(ActionEvent e)
377 taylorColour_actionPerformed(e);
380 hydrophobicityColour.setText("By hydrophobicity");
381 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
383 public void actionPerformed(ActionEvent e)
385 hydrophobicityColour_actionPerformed(e);
388 helixColour.setText("Helix propensity");
389 helixColour.addActionListener(new java.awt.event.ActionListener()
391 public void actionPerformed(ActionEvent e)
393 helixColour_actionPerformed(e);
396 strandColour.setText("Strand propensity");
397 strandColour.addActionListener(new java.awt.event.ActionListener()
399 public void actionPerformed(ActionEvent e)
401 strandColour_actionPerformed(e);
404 turnColour.setText("Turn propensity");
405 turnColour.addActionListener(new java.awt.event.ActionListener()
407 public void actionPerformed(ActionEvent e)
409 turnColour_actionPerformed(e);
412 buriedColour.setText("Buried index");
413 buriedColour.addActionListener(new java.awt.event.ActionListener()
415 public void actionPerformed(ActionEvent e)
417 buriedColour_actionPerformed(e);
420 userDefinedColour.setText("User defined colours");
421 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
423 public void actionPerformed(ActionEvent e)
425 userDefinedColour_actionPerformed(e);
428 PIDColour.setText("Percentage Identity");
429 PIDColour.addActionListener(new java.awt.event.ActionListener()
431 public void actionPerformed(ActionEvent e)
433 PIDColour_actionPerformed(e);
436 BLOSUM62Colour.setText("BLOSUM62 score");
437 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
439 public void actionPerformed(ActionEvent e)
441 BLOSUM62Colour_actionPerformed(e);
444 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
445 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
447 public void actionPerformed(ActionEvent e)
449 avTreeBlosumMenuItem_actionPerformed(e);
452 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
453 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
455 public void actionPerformed(ActionEvent e)
457 njTreeBlosumMenuItem_actionPerformed(e);
460 consensusGraphMenuItem.setActionCommand("");
461 consensusGraphMenuItem.setText("Consensus graph");
462 consensusGraphMenuItem.setState(true);
463 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
465 public void actionPerformed(ActionEvent e)
467 consensusGraphMenuItem_actionPerformed(e);
470 colourTextMenuItem.setText("Colour text");
471 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
473 public void actionPerformed(ActionEvent e)
475 colourTextMenuItem_actionPerformed(e);
478 htmlMenuItem.setText("Output as HTML");
479 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
481 public void actionPerformed(ActionEvent e)
483 htmlMenuItem_actionPerformed(e);
486 overviewMenuItem.setText("Overview window");
487 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
489 public void actionPerformed(ActionEvent e)
491 overviewMenuItem_actionPerformed(e);
494 undoMenuItem.setEnabled(false);
495 undoMenuItem.setMnemonic('Z');
496 undoMenuItem.setText("Undo");
497 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
499 public void actionPerformed(ActionEvent e)
501 undoMenuItem_actionPerformed(e);
504 redoMenuItem.setEnabled(false);
505 redoMenuItem.setMnemonic('0');
506 redoMenuItem.setText("Redo");
507 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
509 public void actionPerformed(ActionEvent e)
511 redoMenuItem_actionPerformed(e);
514 conservationMenuItem.setText("By conservation");
515 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
517 public void actionPerformed(ActionEvent e)
519 conservationMenuItem_actionPerformed(e);
522 noColourmenuItem.setText("None");
523 noColourmenuItem.setSelected(true);
524 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
526 public void actionPerformed(ActionEvent e)
528 noColourmenuItem_actionPerformed(e);
531 wrapMenuItem.setText("Wrap alignment");
532 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
534 public void actionPerformed(ActionEvent e)
536 wrapMenuItem_actionPerformed(e);
539 printMenuItem.setText("Print");
540 printMenuItem.addActionListener(new java.awt.event.ActionListener()
542 public void actionPerformed(ActionEvent e)
544 printMenuItem_actionPerformed(e);
547 renderGapsMenuItem.setText("Render gaps");
548 renderGapsMenuItem.setState(true);
549 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
551 public void actionPerformed(ActionEvent e)
553 renderGapsMenuItem_actionPerformed(e);
556 findMenuItem.setText("Find");
557 findMenuItem.addActionListener(new java.awt.event.ActionListener()
559 public void actionPerformed(ActionEvent e)
561 findMenuItem_actionPerformed(e);
564 searchMenu.setText("Search");
566 abovePIDThreshold.setText("Above PID threshold");
567 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
568 public void actionPerformed(ActionEvent e) {
569 abovePIDThreshold_actionPerformed(e);
572 sequenceFeatures.setText("Sequence Features");
573 sequenceFeatures.addActionListener(new ActionListener()
575 public void actionPerformed(ActionEvent actionEvent)
577 sequenceFeatures_actionPerformed(actionEvent);
580 nucleotideColour.setText("Nucleotide colours");
581 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
583 public void actionPerformed(ActionEvent e)
585 nucleotideColour_actionPerformed(e);
588 deleteGroups.setSelected(false);
589 deleteGroups.setText("Delete all groups");
590 deleteGroups.addActionListener(new java.awt.event.ActionListener()
592 public void actionPerformed(ActionEvent e)
594 deleteGroups_actionPerformed(e);
597 copy.setText("Copy");
598 copy.setMnemonic(KeyEvent.VK_C);
600 copy.addActionListener(new java.awt.event.ActionListener()
602 public void actionPerformed(ActionEvent e)
604 copy_actionPerformed(e);
608 cut.setMnemonic(KeyEvent.VK_X);
609 cut.addActionListener(new java.awt.event.ActionListener()
611 public void actionPerformed(ActionEvent e)
613 cut_actionPerformed(e);
616 delete.setText("Delete");
617 delete.addActionListener(new java.awt.event.ActionListener()
619 public void actionPerformed(ActionEvent e)
621 delete_actionPerformed(e);
624 jMenu1.setMnemonic('V');
625 jMenu1.setText("Paste");
626 pasteNew.setText("to new alignment");
627 pasteNew.addActionListener(new java.awt.event.ActionListener()
629 public void actionPerformed(ActionEvent e)
631 pasteNew_actionPerformed(e);
634 pasteThis.setText("add to this alignment");
635 pasteThis.addActionListener(new java.awt.event.ActionListener()
637 public void actionPerformed(ActionEvent e)
639 pasteThis_actionPerformed(e);
642 applyToAllGroups.setText("Apply colour to all groups");
643 applyToAllGroups.setState(true);
644 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
646 public void actionPerformed(ActionEvent e)
648 applyToAllGroups_actionPerformed(e);
651 createPNG.addActionListener(new java.awt.event.ActionListener()
653 public void actionPerformed(ActionEvent e)
655 createPNG_actionPerformed(e);
658 createPNG.setActionCommand("Save as PNG Image");
659 createPNG.setText("Save as PNG Image");
660 font.setText("Change Font");
661 font.addActionListener(new java.awt.event.ActionListener()
663 public void actionPerformed(ActionEvent e)
665 font_actionPerformed(e);
668 fullSeqId.setText("Show full sequence id");
669 fullSeqId.addActionListener(new java.awt.event.ActionListener()
671 public void actionPerformed(ActionEvent e)
673 fullSeqId_actionPerformed(e);
676 epsFile.setText("Save as EPS file");
677 epsFile.addActionListener(new java.awt.event.ActionListener()
679 public void actionPerformed(ActionEvent e)
681 epsFile_actionPerformed(e);
684 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
685 LoadtreeMenuItem.setText("Load assocated tree");
686 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
687 public void actionPerformed(ActionEvent e)
689 LoadtreeMenuItem_actionPerformed(e);
692 alignFrameMenuBar.add(fileMenu);
693 alignFrameMenuBar.add(editMenu);
694 alignFrameMenuBar.add(searchMenu);
695 alignFrameMenuBar.add(viewMenu);
696 alignFrameMenuBar.add(colourMenu);
697 alignFrameMenuBar.add(calculateMenu);
698 alignFrameMenuBar.add(alignMenu);
699 fileMenu.add(saveAlignmentMenu);
700 fileMenu.add(outputTextboxMenu);
701 fileMenu.add(htmlMenuItem);
702 fileMenu.add(epsFile);
703 fileMenu.add(createPNG);
704 fileMenu.add(printMenuItem);
705 fileMenu.addSeparator();
706 fileMenu.add(LoadtreeMenuItem);
707 fileMenu.addSeparator();
708 fileMenu.add(closeMenuItem);
710 editMenu.add(jMenu1);
712 editMenu.add(delete);
713 editMenu.addSeparator();
714 editMenu.add(undoMenuItem);
715 editMenu.add(redoMenuItem);
716 editMenu.addSeparator();
717 editMenu.add(deselectAllSequenceMenuItem);
718 editMenu.add(selectAllSequenceMenuItem);
719 editMenu.add(invertSequenceMenuItem);
720 editMenu.add(deleteGroups);
721 editMenu.add(groupsMenuItem);
722 editMenu.addSeparator();
723 editMenu.add(deselectAllColumnsMenuItem);
724 editMenu.add(remove2LeftMenuItem);
725 editMenu.add(remove2RightMenuItem);
726 editMenu.addSeparator();
727 editMenu.add(removeGappedColumnMenuItem);
728 editMenu.add(removeAllGapsMenuItem);
729 editMenu.add(setGapCharMenuItem);
730 searchMenu.add(findMenuItem);
732 viewMenu.add(fullSeqId);
733 viewMenu.add(wrapMenuItem);
734 viewMenu.add(viewBoxesMenuItem);
735 viewMenu.add(viewTextMenuItem);
736 viewMenu.add(colourTextMenuItem);
737 viewMenu.add(renderGapsMenuItem);
738 viewMenu.add(consensusGraphMenuItem);
739 viewMenu.add(overviewMenuItem);
740 viewMenu.add(sequenceFeatures);
741 colourMenu.add(applyToAllGroups);
742 colourMenu.add(noColourmenuItem);
743 colourMenu.add(clustalColour);
744 colourMenu.add(zappoColour);
745 colourMenu.add(taylorColour);
746 colourMenu.add(hydrophobicityColour);
747 colourMenu.add(helixColour);
748 colourMenu.add(strandColour);
749 colourMenu.add(turnColour);
750 colourMenu.add(buriedColour);
751 colourMenu.add(nucleotideColour);
752 colourMenu.add(userDefinedColour);
753 colourMenu.add(PIDColour);
754 colourMenu.add(BLOSUM62Colour);
755 colourMenu.addSeparator();
756 colourMenu.add(abovePIDThreshold);
757 colourMenu.add(conservationMenuItem);
758 calculateMenu.add(sortPairwiseMenuItem);
759 calculateMenu.add(sortIDMenuItem);
760 calculateMenu.add(sortGroupMenuItem);
761 calculateMenu.add(sortTreeOrderMenuItem);
762 calculateMenu.add(removeRedundancyMenuItem);
763 calculateMenu.addSeparator();
764 calculateMenu.add(pairwiseAlignmentMenuItem);
765 calculateMenu.add(PCAMenuItem);
766 calculateMenu.addSeparator();
767 calculateMenu.add(averageDistanceTreeMenuItem);
768 calculateMenu.add(neighbourTreeMenuItem);
769 calculateMenu.add(avDistanceTreeBlosumMenuItem);
770 calculateMenu.add(njTreeBlosumMenuItem);
771 alignMenu.add(clustalAlignMenuItem);
772 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
773 jMenu1.add(pasteNew);
774 jMenu1.add(pasteThis);
777 protected void saveAs_actionPerformed(ActionEvent e)
782 protected void outputText_actionPerformed(ActionEvent e)
787 protected void htmlMenuItem_actionPerformed(ActionEvent e)
796 protected void closeMenuItem_actionPerformed(ActionEvent e)
801 protected void redoMenuItem_actionPerformed(ActionEvent e)
806 protected void undoMenuItem_actionPerformed(ActionEvent e)
812 protected void groupsMenuItem_actionPerformed(ActionEvent e)
818 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
823 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
828 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
834 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
839 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
844 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
849 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
854 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
859 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
868 protected void wrapMenuItem_actionPerformed(ActionEvent e)
874 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
879 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
885 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
892 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
897 protected void overviewMenuItem_actionPerformed(ActionEvent e)
902 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
907 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
912 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
917 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
922 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
927 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
932 protected void PCAMenuItem_actionPerformed(ActionEvent e)
937 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
942 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
948 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
953 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
960 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
968 protected void clustalColour_actionPerformed(ActionEvent e)
973 protected void zappoColour_actionPerformed(ActionEvent e)
978 protected void taylorColour_actionPerformed(ActionEvent e)
984 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
989 protected void helixColour_actionPerformed(ActionEvent e)
994 protected void strandColour_actionPerformed(ActionEvent e)
999 protected void turnColour_actionPerformed(ActionEvent e)
1004 protected void buriedColour_actionPerformed(ActionEvent e)
1011 protected void userDefinedColour_actionPerformed(ActionEvent e)
1016 protected void PIDColour_actionPerformed(ActionEvent e)
1021 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1027 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1032 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1038 protected void printMenuItem_actionPerformed(ActionEvent e)
1043 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1048 protected void findMenuItem_actionPerformed(ActionEvent e)
1054 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
1058 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
1063 protected void nucleotideColour_actionPerformed(ActionEvent e)
1068 protected void deleteGroups_actionPerformed(ActionEvent e)
1073 protected void copy_actionPerformed(ActionEvent e)
1079 protected void cut_actionPerformed(ActionEvent e)
1084 protected void delete_actionPerformed(ActionEvent e)
1089 protected void pasteNew_actionPerformed(ActionEvent e)
1094 protected void pasteThis_actionPerformed(ActionEvent e)
1099 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1104 protected void createPNG_actionPerformed(ActionEvent e)
1109 protected void font_actionPerformed(ActionEvent e)
1114 protected void fullSeqId_actionPerformed(ActionEvent e)
1119 protected void epsFile_actionPerformed(ActionEvent e)
1124 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {