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 selectAllSequenceMenuItem = new JMenuItem();
26 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
27 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
28 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
29 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
30 protected JMenuItem remove2RightMenuItem = new JMenuItem();
31 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
32 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
33 protected JMenuItem setGapCharMenuItem = new JMenuItem();
34 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
35 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
36 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
37 protected JMenuItem sortIDMenuItem = new JMenuItem();
38 protected JMenuItem sortGroupMenuItem = new JMenuItem();
39 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
40 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
41 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
42 protected JMenuItem PCAMenuItem = new JMenuItem();
43 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
44 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
45 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
46 BorderLayout borderLayout1 = new BorderLayout();
47 public JLabel statusBar = new JLabel();
48 protected JMenu saveAlignmentMenu = new JMenu();
49 protected JMenu outputTextboxMenu = new JMenu();
50 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
51 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
52 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
53 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
54 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
55 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
56 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
57 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
58 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
59 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
60 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
61 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
62 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
63 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
64 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
65 JMenuItem htmlMenuItem = new JMenuItem();
66 JMenuItem overviewMenuItem = new JMenuItem();
67 protected JMenuItem undoMenuItem = new JMenuItem();
68 protected JMenuItem redoMenuItem = new JMenuItem();
69 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
70 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
71 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
72 JMenuItem printMenuItem = new JMenuItem();
73 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
74 JMenuItem findMenuItem = new JMenuItem();
75 JMenu searchMenu = new JMenu();
76 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
77 protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
78 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
79 JMenuItem deleteGroups = new JMenuItem();
80 JMenuItem delete = new JMenuItem();
81 JMenuItem copy = new JMenuItem();
82 JMenuItem cut = new JMenuItem();
83 JMenu jMenu1 = new JMenu();
84 JMenuItem pasteNew = new JMenuItem();
85 JMenuItem pasteThis = new JMenuItem();
86 protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
87 JMenuItem createPNG = new JMenuItem();
88 protected JMenuItem font = new JMenuItem();
89 protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
90 JMenuItem epsFile = new JMenuItem();
91 JMenuItem LoadtreeMenuItem = new JMenuItem();
92 JMenuItem jpred = 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 selectAllSequenceMenuItem.setText("Select all");
169 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
171 public void actionPerformed(ActionEvent e)
173 selectAllSequenceMenuItem_actionPerformed(e);
176 deselectAllSequenceMenuItem.setText("Clear selection");
177 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
179 public void actionPerformed(ActionEvent e)
181 deselectAllSequenceMenuItem_actionPerformed(e);
184 invertSequenceMenuItem.setText("Invert sequence selection");
185 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
187 public void actionPerformed(ActionEvent e)
189 invertSequenceMenuItem_actionPerformed(e);
192 deselectAllColumnsMenuItem.setText("Deselect all columns");
193 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
195 public void actionPerformed(ActionEvent e)
197 deselectAllColumnsMenuItem_actionPerformed(e);
200 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
201 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
203 public void actionPerformed(ActionEvent e)
205 remove2LeftMenuItem_actionPerformed(e);
208 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
209 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
211 public void actionPerformed(ActionEvent e)
213 remove2RightMenuItem_actionPerformed(e);
216 removeGappedColumnMenuItem.setText("Remove gapped columns");
217 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
219 public void actionPerformed(ActionEvent e)
221 removeGappedColumnMenuItem_actionPerformed(e);
224 removeAllGapsMenuItem.setText("Remove all gaps");
225 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
227 public void actionPerformed(ActionEvent e)
229 removeAllGapsMenuItem_actionPerformed(e);
232 setGapCharMenuItem.setText("Set gap character to \".\"");
233 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
235 public void actionPerformed(ActionEvent e)
237 setGapCharMenuItem_actionPerformed(e);
240 viewBoxesMenuItem.setText("Boxes");
241 viewBoxesMenuItem.setState(true);
242 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
244 public void actionPerformed(ActionEvent e)
246 viewBoxesMenuItem_actionPerformed(e);
249 viewTextMenuItem.setText("Text");
250 viewTextMenuItem.setState(true);
251 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
253 public void actionPerformed(ActionEvent e)
255 viewTextMenuItem_actionPerformed(e);
258 sortPairwiseMenuItem.setText("Sort by pairwise identity");
259 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
261 public void actionPerformed(ActionEvent e)
263 sortPairwiseMenuItem_actionPerformed(e);
266 sortIDMenuItem.setText("Sort by ID");
267 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
269 public void actionPerformed(ActionEvent e)
271 sortIDMenuItem_actionPerformed(e);
274 sortGroupMenuItem.setText("Sort by group");
275 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
277 public void actionPerformed(ActionEvent e)
279 sortGroupMenuItem_actionPerformed(e);
282 sortTreeOrderMenuItem.setText("Sort by tree order");
283 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
285 public void actionPerformed(ActionEvent e)
287 sortTreeOrderMenuItem_actionPerformed(e);
290 removeRedundancyMenuItem.setText("Remove redundancy");
291 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
293 public void actionPerformed(ActionEvent e)
295 removeRedundancyMenuItem_actionPerformed(e);
298 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
299 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
301 public void actionPerformed(ActionEvent e)
303 pairwiseAlignmentMenuItem_actionPerformed(e);
306 PCAMenuItem.setText("Principal component analysis");
307 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
309 public void actionPerformed(ActionEvent e)
311 PCAMenuItem_actionPerformed(e);
314 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
315 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
317 public void actionPerformed(ActionEvent e)
319 averageDistanceTreeMenuItem_actionPerformed(e);
322 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
323 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
325 public void actionPerformed(ActionEvent e)
327 neighbourTreeMenuItem_actionPerformed(e);
330 clustalAlignMenuItem.setText("Clustal alignment");
331 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
333 public void actionPerformed(ActionEvent e)
335 clustalAlignMenuItem_actionPerformed(e);
338 this.getContentPane().setLayout(borderLayout1);
339 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
340 statusBar.setBackground(Color.white);
341 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
342 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
343 statusBar.setText("Status bar");
344 outputTextboxMenu.setMnemonic('T');
345 outputTextboxMenu.setText("Output alignment via textbox");
346 clustalColour.setSelected(false);
347 clustalColour.setText("Clustalx colours");
348 clustalColour.addActionListener(new java.awt.event.ActionListener()
350 public void actionPerformed(ActionEvent e)
352 clustalColour_actionPerformed(e);
355 zappoColour.setText("Zappo colour scheme");
356 zappoColour.addActionListener(new java.awt.event.ActionListener()
358 public void actionPerformed(ActionEvent e)
360 zappoColour_actionPerformed(e);
363 taylorColour.setText("Taylor colour scheme");
364 taylorColour.addActionListener(new java.awt.event.ActionListener()
366 public void actionPerformed(ActionEvent e)
368 taylorColour_actionPerformed(e);
371 hydrophobicityColour.setText("By hydrophobicity");
372 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
374 public void actionPerformed(ActionEvent e)
376 hydrophobicityColour_actionPerformed(e);
379 helixColour.setText("Helix propensity");
380 helixColour.addActionListener(new java.awt.event.ActionListener()
382 public void actionPerformed(ActionEvent e)
384 helixColour_actionPerformed(e);
387 strandColour.setText("Strand propensity");
388 strandColour.addActionListener(new java.awt.event.ActionListener()
390 public void actionPerformed(ActionEvent e)
392 strandColour_actionPerformed(e);
395 turnColour.setText("Turn propensity");
396 turnColour.addActionListener(new java.awt.event.ActionListener()
398 public void actionPerformed(ActionEvent e)
400 turnColour_actionPerformed(e);
403 buriedColour.setText("Buried index");
404 buriedColour.addActionListener(new java.awt.event.ActionListener()
406 public void actionPerformed(ActionEvent e)
408 buriedColour_actionPerformed(e);
411 userDefinedColour.setText("User defined colours");
412 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
414 public void actionPerformed(ActionEvent e)
416 userDefinedColour_actionPerformed(e);
419 PIDColour.setText("Percentage Identity");
420 PIDColour.addActionListener(new java.awt.event.ActionListener()
422 public void actionPerformed(ActionEvent e)
424 PIDColour_actionPerformed(e);
427 BLOSUM62Colour.setText("BLOSUM62 score");
428 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
430 public void actionPerformed(ActionEvent e)
432 BLOSUM62Colour_actionPerformed(e);
435 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
436 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
438 public void actionPerformed(ActionEvent e)
440 avTreeBlosumMenuItem_actionPerformed(e);
443 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
444 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
446 public void actionPerformed(ActionEvent e)
448 njTreeBlosumMenuItem_actionPerformed(e);
451 annotationPanelMenuItem.setActionCommand("");
452 annotationPanelMenuItem.setText("Annotation Panel");
453 annotationPanelMenuItem.setState(true);
454 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
456 public void actionPerformed(ActionEvent e)
458 annotationPanelMenuItem_actionPerformed(e);
461 colourTextMenuItem.setText("Colour text");
462 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
464 public void actionPerformed(ActionEvent e)
466 colourTextMenuItem_actionPerformed(e);
469 htmlMenuItem.setText("Output as HTML");
470 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
472 public void actionPerformed(ActionEvent e)
474 htmlMenuItem_actionPerformed(e);
477 overviewMenuItem.setText("Overview window");
478 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
480 public void actionPerformed(ActionEvent e)
482 overviewMenuItem_actionPerformed(e);
485 undoMenuItem.setEnabled(false);
486 undoMenuItem.setMnemonic('Z');
487 undoMenuItem.setText("Undo");
488 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
490 public void actionPerformed(ActionEvent e)
492 undoMenuItem_actionPerformed(e);
495 redoMenuItem.setEnabled(false);
496 redoMenuItem.setMnemonic('0');
497 redoMenuItem.setText("Redo");
498 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
500 public void actionPerformed(ActionEvent e)
502 redoMenuItem_actionPerformed(e);
505 conservationMenuItem.setText("By conservation");
506 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
508 public void actionPerformed(ActionEvent e)
510 conservationMenuItem_actionPerformed(e);
513 noColourmenuItem.setText("None");
514 noColourmenuItem.setSelected(true);
515 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
517 public void actionPerformed(ActionEvent e)
519 noColourmenuItem_actionPerformed(e);
522 wrapMenuItem.setText("Wrap alignment");
523 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
525 public void actionPerformed(ActionEvent e)
527 wrapMenuItem_actionPerformed(e);
530 printMenuItem.setText("Print");
531 printMenuItem.addActionListener(new java.awt.event.ActionListener()
533 public void actionPerformed(ActionEvent e)
535 printMenuItem_actionPerformed(e);
538 renderGapsMenuItem.setText("Render gaps");
539 renderGapsMenuItem.setState(true);
540 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
542 public void actionPerformed(ActionEvent e)
544 renderGapsMenuItem_actionPerformed(e);
547 findMenuItem.setText("Find");
548 findMenuItem.addActionListener(new java.awt.event.ActionListener()
550 public void actionPerformed(ActionEvent e)
552 findMenuItem_actionPerformed(e);
555 searchMenu.setText("Search");
557 abovePIDThreshold.setText("Above PID threshold");
558 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
559 public void actionPerformed(ActionEvent e) {
560 abovePIDThreshold_actionPerformed(e);
563 sequenceFeatures.setText("Sequence Features");
564 sequenceFeatures.addActionListener(new ActionListener()
566 public void actionPerformed(ActionEvent actionEvent)
568 sequenceFeatures_actionPerformed(actionEvent);
571 nucleotideColour.setText("Nucleotide colours");
572 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
574 public void actionPerformed(ActionEvent e)
576 nucleotideColour_actionPerformed(e);
579 deleteGroups.setSelected(false);
580 deleteGroups.setText("Delete all groups");
581 deleteGroups.addActionListener(new java.awt.event.ActionListener()
583 public void actionPerformed(ActionEvent e)
585 deleteGroups_actionPerformed(e);
588 copy.setText("Copy");
589 copy.setMnemonic(KeyEvent.VK_C);
591 copy.addActionListener(new java.awt.event.ActionListener()
593 public void actionPerformed(ActionEvent e)
595 copy_actionPerformed(e);
599 cut.setMnemonic(KeyEvent.VK_X);
600 cut.addActionListener(new java.awt.event.ActionListener()
602 public void actionPerformed(ActionEvent e)
604 cut_actionPerformed(e);
607 delete.setText("Delete");
608 delete.addActionListener(new java.awt.event.ActionListener()
610 public void actionPerformed(ActionEvent e)
612 delete_actionPerformed(e);
615 jMenu1.setMnemonic('V');
616 jMenu1.setText("Paste");
617 pasteNew.setText("to new alignment");
618 pasteNew.addActionListener(new java.awt.event.ActionListener()
620 public void actionPerformed(ActionEvent e)
622 pasteNew_actionPerformed(e);
625 pasteThis.setText("add to this alignment");
626 pasteThis.addActionListener(new java.awt.event.ActionListener()
628 public void actionPerformed(ActionEvent e)
630 pasteThis_actionPerformed(e);
633 applyToAllGroups.setText("Apply colour to all groups");
634 applyToAllGroups.setState(true);
635 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
637 public void actionPerformed(ActionEvent e)
639 applyToAllGroups_actionPerformed(e);
642 createPNG.addActionListener(new java.awt.event.ActionListener()
644 public void actionPerformed(ActionEvent e)
646 createPNG_actionPerformed(e);
649 createPNG.setActionCommand("Save as PNG Image");
650 createPNG.setText("Save as PNG Image");
651 font.setText("Change Font");
652 font.addActionListener(new java.awt.event.ActionListener()
654 public void actionPerformed(ActionEvent e)
656 font_actionPerformed(e);
659 fullSeqId.setText("Show full sequence id");
660 fullSeqId.addActionListener(new java.awt.event.ActionListener()
662 public void actionPerformed(ActionEvent e)
664 fullSeqId_actionPerformed(e);
667 epsFile.setText("Save as EPS file");
668 epsFile.addActionListener(new java.awt.event.ActionListener()
670 public void actionPerformed(ActionEvent e)
672 epsFile_actionPerformed(e);
675 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
676 LoadtreeMenuItem.setText("Load assocated tree");
677 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
678 public void actionPerformed(ActionEvent e)
680 LoadtreeMenuItem_actionPerformed(e);
683 jpred.setText("JPred");
684 jpred.addActionListener(new java.awt.event.ActionListener()
686 public void actionPerformed(ActionEvent e)
688 jpred_actionPerformed(e);
691 alignFrameMenuBar.add(fileMenu);
692 alignFrameMenuBar.add(editMenu);
693 alignFrameMenuBar.add(searchMenu);
694 alignFrameMenuBar.add(viewMenu);
695 alignFrameMenuBar.add(colourMenu);
696 alignFrameMenuBar.add(calculateMenu);
697 alignFrameMenuBar.add(alignMenu);
698 fileMenu.add(saveAlignmentMenu);
699 fileMenu.add(outputTextboxMenu);
700 fileMenu.add(htmlMenuItem);
701 fileMenu.add(epsFile);
702 fileMenu.add(createPNG);
703 fileMenu.add(printMenuItem);
704 fileMenu.addSeparator();
705 fileMenu.add(LoadtreeMenuItem);
706 fileMenu.addSeparator();
707 fileMenu.add(closeMenuItem);
709 editMenu.add(jMenu1);
711 editMenu.add(delete);
712 editMenu.addSeparator();
713 editMenu.add(undoMenuItem);
714 editMenu.add(redoMenuItem);
715 editMenu.addSeparator();
716 editMenu.add(deselectAllSequenceMenuItem);
717 editMenu.add(selectAllSequenceMenuItem);
718 editMenu.add(invertSequenceMenuItem);
719 editMenu.add(deleteGroups);
720 editMenu.addSeparator();
721 editMenu.add(deselectAllColumnsMenuItem);
722 editMenu.add(remove2LeftMenuItem);
723 editMenu.add(remove2RightMenuItem);
724 editMenu.addSeparator();
725 editMenu.add(removeGappedColumnMenuItem);
726 editMenu.add(removeAllGapsMenuItem);
727 editMenu.add(setGapCharMenuItem);
728 searchMenu.add(findMenuItem);
730 viewMenu.add(fullSeqId);
731 viewMenu.add(wrapMenuItem);
732 viewMenu.add(viewBoxesMenuItem);
733 viewMenu.add(viewTextMenuItem);
734 viewMenu.add(colourTextMenuItem);
735 viewMenu.add(renderGapsMenuItem);
736 viewMenu.add(annotationPanelMenuItem);
737 viewMenu.add(overviewMenuItem);
738 viewMenu.add(sequenceFeatures);
739 colourMenu.add(applyToAllGroups);
740 colourMenu.add(noColourmenuItem);
741 colourMenu.add(clustalColour);
742 colourMenu.add(zappoColour);
743 colourMenu.add(taylorColour);
744 colourMenu.add(hydrophobicityColour);
745 colourMenu.add(helixColour);
746 colourMenu.add(strandColour);
747 colourMenu.add(turnColour);
748 colourMenu.add(buriedColour);
749 colourMenu.add(nucleotideColour);
750 colourMenu.add(userDefinedColour);
751 colourMenu.add(PIDColour);
752 colourMenu.add(BLOSUM62Colour);
753 colourMenu.addSeparator();
754 colourMenu.add(abovePIDThreshold);
755 colourMenu.add(conservationMenuItem);
756 calculateMenu.add(sortPairwiseMenuItem);
757 calculateMenu.add(sortIDMenuItem);
758 calculateMenu.add(sortGroupMenuItem);
759 calculateMenu.add(sortTreeOrderMenuItem);
760 calculateMenu.add(removeRedundancyMenuItem);
761 calculateMenu.addSeparator();
762 calculateMenu.add(pairwiseAlignmentMenuItem);
763 calculateMenu.add(PCAMenuItem);
764 calculateMenu.addSeparator();
765 calculateMenu.add(averageDistanceTreeMenuItem);
766 calculateMenu.add(neighbourTreeMenuItem);
767 calculateMenu.add(avDistanceTreeBlosumMenuItem);
768 calculateMenu.add(njTreeBlosumMenuItem);
769 alignMenu.add(clustalAlignMenuItem);
770 alignMenu.add(jpred);
771 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
772 jMenu1.add(pasteNew);
773 jMenu1.add(pasteThis);
776 protected void saveAs_actionPerformed(ActionEvent e)
781 protected void outputText_actionPerformed(ActionEvent e)
786 protected void htmlMenuItem_actionPerformed(ActionEvent e)
795 protected void closeMenuItem_actionPerformed(ActionEvent e)
800 protected void redoMenuItem_actionPerformed(ActionEvent e)
805 protected void undoMenuItem_actionPerformed(ActionEvent e)
813 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
818 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
823 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
829 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
834 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
839 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
844 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
849 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
854 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
863 protected void wrapMenuItem_actionPerformed(ActionEvent e)
869 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
874 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
880 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
887 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
892 protected void overviewMenuItem_actionPerformed(ActionEvent e)
897 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
902 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
907 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
912 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
917 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
922 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
927 protected void PCAMenuItem_actionPerformed(ActionEvent e)
932 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
937 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
943 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
948 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
955 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
963 protected void clustalColour_actionPerformed(ActionEvent e)
968 protected void zappoColour_actionPerformed(ActionEvent e)
973 protected void taylorColour_actionPerformed(ActionEvent e)
979 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
984 protected void helixColour_actionPerformed(ActionEvent e)
989 protected void strandColour_actionPerformed(ActionEvent e)
994 protected void turnColour_actionPerformed(ActionEvent e)
999 protected void buriedColour_actionPerformed(ActionEvent e)
1006 protected void userDefinedColour_actionPerformed(ActionEvent e)
1011 protected void PIDColour_actionPerformed(ActionEvent e)
1016 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1022 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1027 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1033 protected void printMenuItem_actionPerformed(ActionEvent e)
1038 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1043 protected void findMenuItem_actionPerformed(ActionEvent e)
1049 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
1053 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
1058 protected void nucleotideColour_actionPerformed(ActionEvent e)
1063 protected void deleteGroups_actionPerformed(ActionEvent e)
1068 protected void copy_actionPerformed(ActionEvent e)
1074 protected void cut_actionPerformed(ActionEvent e)
1079 protected void delete_actionPerformed(ActionEvent e)
1084 protected void pasteNew_actionPerformed(ActionEvent e)
1089 protected void pasteThis_actionPerformed(ActionEvent e)
1094 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1099 protected void createPNG_actionPerformed(ActionEvent e)
1104 protected void font_actionPerformed(ActionEvent e)
1109 protected void fullSeqId_actionPerformed(ActionEvent e)
1114 protected void epsFile_actionPerformed(ActionEvent e)
1119 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1123 protected void jpred_actionPerformed(ActionEvent e)