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 annotationPanelMenuItem = 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();
93 JMenuItem jpred = new JMenuItem();
101 setJMenuBar(alignFrameMenuBar);
104 // dynamically fill save as menu with available formats
105 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
106 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
107 saveAlignmentMenu.add( item );
108 item.addActionListener(new java.awt.event.ActionListener()
110 public void actionPerformed(ActionEvent e)
112 saveAs_actionPerformed(e);
116 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
117 item.addActionListener(new java.awt.event.ActionListener()
119 public void actionPerformed(ActionEvent e)
121 outputText_actionPerformed(e);
125 outputTextboxMenu.add( item );
134 ButtonGroup colours = new ButtonGroup();
135 colours.add(noColourmenuItem);
136 colours.add(clustalColour);
137 colours.add(zappoColour);
138 colours.add(taylorColour);
139 colours.add(hydrophobicityColour);
140 colours.add(helixColour);
141 colours.add(strandColour);
142 colours.add(turnColour);
143 colours.add(buriedColour);
144 colours.add(userDefinedColour);
145 colours.add(PIDColour);
146 colours.add(BLOSUM62Colour);
147 colours.add(nucleotideColour);
149 private void jbInit() throws Exception
151 fileMenu.setMnemonic('F');
152 fileMenu.setText("File");
153 saveAlignmentMenu.setMnemonic('L');
154 saveAlignmentMenu.setText("Save alignment to local file");
155 closeMenuItem.setMnemonic('C');
156 closeMenuItem.setText("Close");
157 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
159 public void actionPerformed(ActionEvent e)
161 closeMenuItem_actionPerformed(e);
164 editMenu.setText("Edit");
165 viewMenu.setText("View");
166 colourMenu.setText("Colour");
167 calculateMenu.setText("Calculate");
168 alignMenu.setText("Web Service");
169 groupsMenuItem.setVisible(false);
170 groupsMenuItem.setText("Groups");
171 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
173 public void actionPerformed(ActionEvent e)
175 groupsMenuItem_actionPerformed(e);
178 selectAllSequenceMenuItem.setText("Select all");
179 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
181 public void actionPerformed(ActionEvent e)
183 selectAllSequenceMenuItem_actionPerformed(e);
186 deselectAllSequenceMenuItem.setText("Clear selection");
187 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
189 public void actionPerformed(ActionEvent e)
191 deselectAllSequenceMenuItem_actionPerformed(e);
194 invertSequenceMenuItem.setText("Invert sequence selection");
195 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
197 public void actionPerformed(ActionEvent e)
199 invertSequenceMenuItem_actionPerformed(e);
202 deselectAllColumnsMenuItem.setText("Deselect all columns");
203 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
205 public void actionPerformed(ActionEvent e)
207 deselectAllColumnsMenuItem_actionPerformed(e);
210 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
211 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
213 public void actionPerformed(ActionEvent e)
215 remove2LeftMenuItem_actionPerformed(e);
218 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
219 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
221 public void actionPerformed(ActionEvent e)
223 remove2RightMenuItem_actionPerformed(e);
226 removeGappedColumnMenuItem.setText("Remove gapped columns");
227 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
229 public void actionPerformed(ActionEvent e)
231 removeGappedColumnMenuItem_actionPerformed(e);
234 removeAllGapsMenuItem.setText("Remove all gaps");
235 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
237 public void actionPerformed(ActionEvent e)
239 removeAllGapsMenuItem_actionPerformed(e);
242 setGapCharMenuItem.setText("Set gap character to \".\"");
243 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
245 public void actionPerformed(ActionEvent e)
247 setGapCharMenuItem_actionPerformed(e);
250 viewBoxesMenuItem.setText("Boxes");
251 viewBoxesMenuItem.setState(true);
252 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
254 public void actionPerformed(ActionEvent e)
256 viewBoxesMenuItem_actionPerformed(e);
259 viewTextMenuItem.setText("Text");
260 viewTextMenuItem.setState(true);
261 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
263 public void actionPerformed(ActionEvent e)
265 viewTextMenuItem_actionPerformed(e);
268 sortPairwiseMenuItem.setText("Sort by pairwise identity");
269 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
271 public void actionPerformed(ActionEvent e)
273 sortPairwiseMenuItem_actionPerformed(e);
276 sortIDMenuItem.setText("Sort by ID");
277 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
279 public void actionPerformed(ActionEvent e)
281 sortIDMenuItem_actionPerformed(e);
284 sortGroupMenuItem.setText("Sort by group");
285 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
287 public void actionPerformed(ActionEvent e)
289 sortGroupMenuItem_actionPerformed(e);
292 sortTreeOrderMenuItem.setText("Sort by tree order");
293 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
295 public void actionPerformed(ActionEvent e)
297 sortTreeOrderMenuItem_actionPerformed(e);
300 removeRedundancyMenuItem.setText("Remove redundancy");
301 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
303 public void actionPerformed(ActionEvent e)
305 removeRedundancyMenuItem_actionPerformed(e);
308 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
309 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
311 public void actionPerformed(ActionEvent e)
313 pairwiseAlignmentMenuItem_actionPerformed(e);
316 PCAMenuItem.setText("Principal component analysis");
317 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
319 public void actionPerformed(ActionEvent e)
321 PCAMenuItem_actionPerformed(e);
324 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
325 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
327 public void actionPerformed(ActionEvent e)
329 averageDistanceTreeMenuItem_actionPerformed(e);
332 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
333 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
335 public void actionPerformed(ActionEvent e)
337 neighbourTreeMenuItem_actionPerformed(e);
340 clustalAlignMenuItem.setText("Clustal alignment");
341 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
343 public void actionPerformed(ActionEvent e)
345 clustalAlignMenuItem_actionPerformed(e);
348 this.getContentPane().setLayout(borderLayout1);
349 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
350 statusBar.setBackground(Color.white);
351 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
352 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
353 statusBar.setText("Status bar");
354 outputTextboxMenu.setMnemonic('T');
355 outputTextboxMenu.setText("Output alignment via textbox");
356 clustalColour.setSelected(false);
357 clustalColour.setText("Clustalx colours");
358 clustalColour.addActionListener(new java.awt.event.ActionListener()
360 public void actionPerformed(ActionEvent e)
362 clustalColour_actionPerformed(e);
365 zappoColour.setText("Zappo colour scheme");
366 zappoColour.addActionListener(new java.awt.event.ActionListener()
368 public void actionPerformed(ActionEvent e)
370 zappoColour_actionPerformed(e);
373 taylorColour.setText("Taylor colour scheme");
374 taylorColour.addActionListener(new java.awt.event.ActionListener()
376 public void actionPerformed(ActionEvent e)
378 taylorColour_actionPerformed(e);
381 hydrophobicityColour.setText("By hydrophobicity");
382 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
384 public void actionPerformed(ActionEvent e)
386 hydrophobicityColour_actionPerformed(e);
389 helixColour.setText("Helix propensity");
390 helixColour.addActionListener(new java.awt.event.ActionListener()
392 public void actionPerformed(ActionEvent e)
394 helixColour_actionPerformed(e);
397 strandColour.setText("Strand propensity");
398 strandColour.addActionListener(new java.awt.event.ActionListener()
400 public void actionPerformed(ActionEvent e)
402 strandColour_actionPerformed(e);
405 turnColour.setText("Turn propensity");
406 turnColour.addActionListener(new java.awt.event.ActionListener()
408 public void actionPerformed(ActionEvent e)
410 turnColour_actionPerformed(e);
413 buriedColour.setText("Buried index");
414 buriedColour.addActionListener(new java.awt.event.ActionListener()
416 public void actionPerformed(ActionEvent e)
418 buriedColour_actionPerformed(e);
421 userDefinedColour.setText("User defined colours");
422 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
424 public void actionPerformed(ActionEvent e)
426 userDefinedColour_actionPerformed(e);
429 PIDColour.setText("Percentage Identity");
430 PIDColour.addActionListener(new java.awt.event.ActionListener()
432 public void actionPerformed(ActionEvent e)
434 PIDColour_actionPerformed(e);
437 BLOSUM62Colour.setText("BLOSUM62 score");
438 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
440 public void actionPerformed(ActionEvent e)
442 BLOSUM62Colour_actionPerformed(e);
445 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
446 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
448 public void actionPerformed(ActionEvent e)
450 avTreeBlosumMenuItem_actionPerformed(e);
453 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
454 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
456 public void actionPerformed(ActionEvent e)
458 njTreeBlosumMenuItem_actionPerformed(e);
461 annotationPanelMenuItem.setActionCommand("");
462 annotationPanelMenuItem.setText("Annotation Panel");
463 annotationPanelMenuItem.setState(true);
464 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
466 public void actionPerformed(ActionEvent e)
468 annotationPanelMenuItem_actionPerformed(e);
471 colourTextMenuItem.setText("Colour text");
472 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
474 public void actionPerformed(ActionEvent e)
476 colourTextMenuItem_actionPerformed(e);
479 htmlMenuItem.setText("Output as HTML");
480 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
482 public void actionPerformed(ActionEvent e)
484 htmlMenuItem_actionPerformed(e);
487 overviewMenuItem.setText("Overview window");
488 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
490 public void actionPerformed(ActionEvent e)
492 overviewMenuItem_actionPerformed(e);
495 undoMenuItem.setEnabled(false);
496 undoMenuItem.setMnemonic('Z');
497 undoMenuItem.setText("Undo");
498 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
500 public void actionPerformed(ActionEvent e)
502 undoMenuItem_actionPerformed(e);
505 redoMenuItem.setEnabled(false);
506 redoMenuItem.setMnemonic('0');
507 redoMenuItem.setText("Redo");
508 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
510 public void actionPerformed(ActionEvent e)
512 redoMenuItem_actionPerformed(e);
515 conservationMenuItem.setText("By conservation");
516 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
518 public void actionPerformed(ActionEvent e)
520 conservationMenuItem_actionPerformed(e);
523 noColourmenuItem.setText("None");
524 noColourmenuItem.setSelected(true);
525 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
527 public void actionPerformed(ActionEvent e)
529 noColourmenuItem_actionPerformed(e);
532 wrapMenuItem.setText("Wrap alignment");
533 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
535 public void actionPerformed(ActionEvent e)
537 wrapMenuItem_actionPerformed(e);
540 printMenuItem.setText("Print");
541 printMenuItem.addActionListener(new java.awt.event.ActionListener()
543 public void actionPerformed(ActionEvent e)
545 printMenuItem_actionPerformed(e);
548 renderGapsMenuItem.setText("Render gaps");
549 renderGapsMenuItem.setState(true);
550 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
552 public void actionPerformed(ActionEvent e)
554 renderGapsMenuItem_actionPerformed(e);
557 findMenuItem.setText("Find");
558 findMenuItem.addActionListener(new java.awt.event.ActionListener()
560 public void actionPerformed(ActionEvent e)
562 findMenuItem_actionPerformed(e);
565 searchMenu.setText("Search");
567 abovePIDThreshold.setText("Above PID threshold");
568 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
569 public void actionPerformed(ActionEvent e) {
570 abovePIDThreshold_actionPerformed(e);
573 sequenceFeatures.setText("Sequence Features");
574 sequenceFeatures.addActionListener(new ActionListener()
576 public void actionPerformed(ActionEvent actionEvent)
578 sequenceFeatures_actionPerformed(actionEvent);
581 nucleotideColour.setText("Nucleotide colours");
582 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
584 public void actionPerformed(ActionEvent e)
586 nucleotideColour_actionPerformed(e);
589 deleteGroups.setSelected(false);
590 deleteGroups.setText("Delete all groups");
591 deleteGroups.addActionListener(new java.awt.event.ActionListener()
593 public void actionPerformed(ActionEvent e)
595 deleteGroups_actionPerformed(e);
598 copy.setText("Copy");
599 copy.setMnemonic(KeyEvent.VK_C);
601 copy.addActionListener(new java.awt.event.ActionListener()
603 public void actionPerformed(ActionEvent e)
605 copy_actionPerformed(e);
609 cut.setMnemonic(KeyEvent.VK_X);
610 cut.addActionListener(new java.awt.event.ActionListener()
612 public void actionPerformed(ActionEvent e)
614 cut_actionPerformed(e);
617 delete.setText("Delete");
618 delete.addActionListener(new java.awt.event.ActionListener()
620 public void actionPerformed(ActionEvent e)
622 delete_actionPerformed(e);
625 jMenu1.setMnemonic('V');
626 jMenu1.setText("Paste");
627 pasteNew.setText("to new alignment");
628 pasteNew.addActionListener(new java.awt.event.ActionListener()
630 public void actionPerformed(ActionEvent e)
632 pasteNew_actionPerformed(e);
635 pasteThis.setText("add to this alignment");
636 pasteThis.addActionListener(new java.awt.event.ActionListener()
638 public void actionPerformed(ActionEvent e)
640 pasteThis_actionPerformed(e);
643 applyToAllGroups.setText("Apply colour to all groups");
644 applyToAllGroups.setState(true);
645 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
647 public void actionPerformed(ActionEvent e)
649 applyToAllGroups_actionPerformed(e);
652 createPNG.addActionListener(new java.awt.event.ActionListener()
654 public void actionPerformed(ActionEvent e)
656 createPNG_actionPerformed(e);
659 createPNG.setActionCommand("Save as PNG Image");
660 createPNG.setText("Save as PNG Image");
661 font.setText("Change Font");
662 font.addActionListener(new java.awt.event.ActionListener()
664 public void actionPerformed(ActionEvent e)
666 font_actionPerformed(e);
669 fullSeqId.setText("Show full sequence id");
670 fullSeqId.addActionListener(new java.awt.event.ActionListener()
672 public void actionPerformed(ActionEvent e)
674 fullSeqId_actionPerformed(e);
677 epsFile.setText("Save as EPS file");
678 epsFile.addActionListener(new java.awt.event.ActionListener()
680 public void actionPerformed(ActionEvent e)
682 epsFile_actionPerformed(e);
685 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
686 LoadtreeMenuItem.setText("Load assocated tree");
687 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
688 public void actionPerformed(ActionEvent e)
690 LoadtreeMenuItem_actionPerformed(e);
693 jpred.setText("JPred");
694 jpred.addActionListener(new java.awt.event.ActionListener()
696 public void actionPerformed(ActionEvent e)
698 jpred_actionPerformed(e);
701 alignFrameMenuBar.add(fileMenu);
702 alignFrameMenuBar.add(editMenu);
703 alignFrameMenuBar.add(searchMenu);
704 alignFrameMenuBar.add(viewMenu);
705 alignFrameMenuBar.add(colourMenu);
706 alignFrameMenuBar.add(calculateMenu);
707 alignFrameMenuBar.add(alignMenu);
708 fileMenu.add(saveAlignmentMenu);
709 fileMenu.add(outputTextboxMenu);
710 fileMenu.add(htmlMenuItem);
711 fileMenu.add(epsFile);
712 fileMenu.add(createPNG);
713 fileMenu.add(printMenuItem);
714 fileMenu.addSeparator();
715 fileMenu.add(LoadtreeMenuItem);
716 fileMenu.addSeparator();
717 fileMenu.add(closeMenuItem);
719 editMenu.add(jMenu1);
721 editMenu.add(delete);
722 editMenu.addSeparator();
723 editMenu.add(undoMenuItem);
724 editMenu.add(redoMenuItem);
725 editMenu.addSeparator();
726 editMenu.add(deselectAllSequenceMenuItem);
727 editMenu.add(selectAllSequenceMenuItem);
728 editMenu.add(invertSequenceMenuItem);
729 editMenu.add(deleteGroups);
730 editMenu.add(groupsMenuItem);
731 editMenu.addSeparator();
732 editMenu.add(deselectAllColumnsMenuItem);
733 editMenu.add(remove2LeftMenuItem);
734 editMenu.add(remove2RightMenuItem);
735 editMenu.addSeparator();
736 editMenu.add(removeGappedColumnMenuItem);
737 editMenu.add(removeAllGapsMenuItem);
738 editMenu.add(setGapCharMenuItem);
739 searchMenu.add(findMenuItem);
741 viewMenu.add(fullSeqId);
742 viewMenu.add(wrapMenuItem);
743 viewMenu.add(viewBoxesMenuItem);
744 viewMenu.add(viewTextMenuItem);
745 viewMenu.add(colourTextMenuItem);
746 viewMenu.add(renderGapsMenuItem);
747 viewMenu.add(annotationPanelMenuItem);
748 viewMenu.add(overviewMenuItem);
749 viewMenu.add(sequenceFeatures);
750 colourMenu.add(applyToAllGroups);
751 colourMenu.add(noColourmenuItem);
752 colourMenu.add(clustalColour);
753 colourMenu.add(zappoColour);
754 colourMenu.add(taylorColour);
755 colourMenu.add(hydrophobicityColour);
756 colourMenu.add(helixColour);
757 colourMenu.add(strandColour);
758 colourMenu.add(turnColour);
759 colourMenu.add(buriedColour);
760 colourMenu.add(nucleotideColour);
761 colourMenu.add(userDefinedColour);
762 colourMenu.add(PIDColour);
763 colourMenu.add(BLOSUM62Colour);
764 colourMenu.addSeparator();
765 colourMenu.add(abovePIDThreshold);
766 colourMenu.add(conservationMenuItem);
767 calculateMenu.add(sortPairwiseMenuItem);
768 calculateMenu.add(sortIDMenuItem);
769 calculateMenu.add(sortGroupMenuItem);
770 calculateMenu.add(sortTreeOrderMenuItem);
771 calculateMenu.add(removeRedundancyMenuItem);
772 calculateMenu.addSeparator();
773 calculateMenu.add(pairwiseAlignmentMenuItem);
774 calculateMenu.add(PCAMenuItem);
775 calculateMenu.addSeparator();
776 calculateMenu.add(averageDistanceTreeMenuItem);
777 calculateMenu.add(neighbourTreeMenuItem);
778 calculateMenu.add(avDistanceTreeBlosumMenuItem);
779 calculateMenu.add(njTreeBlosumMenuItem);
780 alignMenu.add(clustalAlignMenuItem);
781 alignMenu.add(jpred);
782 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
783 jMenu1.add(pasteNew);
784 jMenu1.add(pasteThis);
787 protected void saveAs_actionPerformed(ActionEvent e)
792 protected void outputText_actionPerformed(ActionEvent e)
797 protected void htmlMenuItem_actionPerformed(ActionEvent e)
806 protected void closeMenuItem_actionPerformed(ActionEvent e)
811 protected void redoMenuItem_actionPerformed(ActionEvent e)
816 protected void undoMenuItem_actionPerformed(ActionEvent e)
822 protected void groupsMenuItem_actionPerformed(ActionEvent e)
828 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
833 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
838 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
844 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
849 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
854 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
859 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
864 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
869 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
878 protected void wrapMenuItem_actionPerformed(ActionEvent e)
884 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
889 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
895 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
902 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
907 protected void overviewMenuItem_actionPerformed(ActionEvent e)
912 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
917 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
922 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
927 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
932 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
937 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
942 protected void PCAMenuItem_actionPerformed(ActionEvent e)
947 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
952 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
958 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
963 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
970 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
978 protected void clustalColour_actionPerformed(ActionEvent e)
983 protected void zappoColour_actionPerformed(ActionEvent e)
988 protected void taylorColour_actionPerformed(ActionEvent e)
994 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
999 protected void helixColour_actionPerformed(ActionEvent e)
1004 protected void strandColour_actionPerformed(ActionEvent e)
1009 protected void turnColour_actionPerformed(ActionEvent e)
1014 protected void buriedColour_actionPerformed(ActionEvent e)
1021 protected void userDefinedColour_actionPerformed(ActionEvent e)
1026 protected void PIDColour_actionPerformed(ActionEvent e)
1031 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1037 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1042 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1048 protected void printMenuItem_actionPerformed(ActionEvent e)
1053 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1058 protected void findMenuItem_actionPerformed(ActionEvent e)
1064 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
1068 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
1073 protected void nucleotideColour_actionPerformed(ActionEvent e)
1078 protected void deleteGroups_actionPerformed(ActionEvent e)
1083 protected void copy_actionPerformed(ActionEvent e)
1089 protected void cut_actionPerformed(ActionEvent e)
1094 protected void delete_actionPerformed(ActionEvent e)
1099 protected void pasteNew_actionPerformed(ActionEvent e)
1104 protected void pasteThis_actionPerformed(ActionEvent e)
1109 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1114 protected void createPNG_actionPerformed(ActionEvent e)
1119 protected void font_actionPerformed(ActionEvent e)
1124 protected void fullSeqId_actionPerformed(ActionEvent e)
1129 protected void epsFile_actionPerformed(ActionEvent e)
1134 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1138 protected void jpred_actionPerformed(ActionEvent e)