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();
93 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
94 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
95 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
103 setJMenuBar(alignFrameMenuBar);
106 // dynamically fill save as menu with available formats
107 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
108 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
109 saveAlignmentMenu.add( item );
110 item.addActionListener(new java.awt.event.ActionListener()
112 public void actionPerformed(ActionEvent e)
114 saveAs_actionPerformed(e);
118 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
119 item.addActionListener(new java.awt.event.ActionListener()
121 public void actionPerformed(ActionEvent e)
123 outputText_actionPerformed(e);
127 outputTextboxMenu.add( item );
136 ButtonGroup colours = new ButtonGroup();
137 colours.add(noColourmenuItem);
138 colours.add(clustalColour);
139 colours.add(zappoColour);
140 colours.add(taylorColour);
141 colours.add(hydrophobicityColour);
142 colours.add(helixColour);
143 colours.add(strandColour);
144 colours.add(turnColour);
145 colours.add(buriedColour);
146 colours.add(userDefinedColour);
147 colours.add(PIDColour);
148 colours.add(BLOSUM62Colour);
149 colours.add(nucleotideColour);
151 private void jbInit() throws Exception
153 fileMenu.setMnemonic('F');
154 fileMenu.setText("File");
155 saveAlignmentMenu.setMnemonic('L');
156 saveAlignmentMenu.setText("Save alignment to local file");
157 closeMenuItem.setMnemonic('C');
158 closeMenuItem.setText("Close");
159 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
161 public void actionPerformed(ActionEvent e)
163 closeMenuItem_actionPerformed(e);
166 editMenu.setText("Edit");
167 viewMenu.setText("View");
168 colourMenu.setText("Colour");
169 calculateMenu.setText("Calculate");
170 alignMenu.setText("Web Service");
171 selectAllSequenceMenuItem.setText("Select all");
172 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
174 public void actionPerformed(ActionEvent e)
176 selectAllSequenceMenuItem_actionPerformed(e);
179 deselectAllSequenceMenuItem.setText("Clear selection");
180 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
182 public void actionPerformed(ActionEvent e)
184 deselectAllSequenceMenuItem_actionPerformed(e);
187 invertSequenceMenuItem.setText("Invert sequence selection");
188 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
190 public void actionPerformed(ActionEvent e)
192 invertSequenceMenuItem_actionPerformed(e);
195 deselectAllColumnsMenuItem.setText("Deselect all columns");
196 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
198 public void actionPerformed(ActionEvent e)
200 deselectAllColumnsMenuItem_actionPerformed(e);
203 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
204 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
206 public void actionPerformed(ActionEvent e)
208 remove2LeftMenuItem_actionPerformed(e);
211 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
212 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
214 public void actionPerformed(ActionEvent e)
216 remove2RightMenuItem_actionPerformed(e);
219 removeGappedColumnMenuItem.setText("Remove gapped columns");
220 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
222 public void actionPerformed(ActionEvent e)
224 removeGappedColumnMenuItem_actionPerformed(e);
227 removeAllGapsMenuItem.setText("Remove all gaps");
228 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
230 public void actionPerformed(ActionEvent e)
232 removeAllGapsMenuItem_actionPerformed(e);
235 setGapCharMenuItem.setText("Set gap character to \".\"");
236 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
238 public void actionPerformed(ActionEvent e)
240 setGapCharMenuItem_actionPerformed(e);
243 viewBoxesMenuItem.setText("Boxes");
244 viewBoxesMenuItem.setState(true);
245 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
247 public void actionPerformed(ActionEvent e)
249 viewBoxesMenuItem_actionPerformed(e);
252 viewTextMenuItem.setText("Text");
253 viewTextMenuItem.setState(true);
254 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
256 public void actionPerformed(ActionEvent e)
258 viewTextMenuItem_actionPerformed(e);
261 sortPairwiseMenuItem.setText("Sort by pairwise identity");
262 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
264 public void actionPerformed(ActionEvent e)
266 sortPairwiseMenuItem_actionPerformed(e);
269 sortIDMenuItem.setText("Sort by ID");
270 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
272 public void actionPerformed(ActionEvent e)
274 sortIDMenuItem_actionPerformed(e);
277 sortGroupMenuItem.setText("Sort by group");
278 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
280 public void actionPerformed(ActionEvent e)
282 sortGroupMenuItem_actionPerformed(e);
285 sortTreeOrderMenuItem.setText("Sort by tree order");
286 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
288 public void actionPerformed(ActionEvent e)
290 sortTreeOrderMenuItem_actionPerformed(e);
293 removeRedundancyMenuItem.setText("Remove redundancy");
294 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
296 public void actionPerformed(ActionEvent e)
298 removeRedundancyMenuItem_actionPerformed(e);
301 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
302 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
304 public void actionPerformed(ActionEvent e)
306 pairwiseAlignmentMenuItem_actionPerformed(e);
309 PCAMenuItem.setText("Principal component analysis");
310 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
312 public void actionPerformed(ActionEvent e)
314 PCAMenuItem_actionPerformed(e);
317 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
318 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
320 public void actionPerformed(ActionEvent e)
322 averageDistanceTreeMenuItem_actionPerformed(e);
325 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
326 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
328 public void actionPerformed(ActionEvent e)
330 neighbourTreeMenuItem_actionPerformed(e);
333 clustalAlignMenuItem.setText("Clustal alignment");
334 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
336 public void actionPerformed(ActionEvent e)
338 clustalAlignMenuItem_actionPerformed(e);
341 this.getContentPane().setLayout(borderLayout1);
342 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
343 statusBar.setBackground(Color.white);
344 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
345 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
346 statusBar.setText("Status bar");
347 outputTextboxMenu.setMnemonic('T');
348 outputTextboxMenu.setText("Output alignment via textbox");
349 clustalColour.setSelected(false);
350 clustalColour.setText("Clustalx colours");
351 clustalColour.addActionListener(new java.awt.event.ActionListener()
353 public void actionPerformed(ActionEvent e)
355 clustalColour_actionPerformed(e);
358 zappoColour.setText("Zappo colour scheme");
359 zappoColour.addActionListener(new java.awt.event.ActionListener()
361 public void actionPerformed(ActionEvent e)
363 zappoColour_actionPerformed(e);
366 taylorColour.setText("Taylor colour scheme");
367 taylorColour.addActionListener(new java.awt.event.ActionListener()
369 public void actionPerformed(ActionEvent e)
371 taylorColour_actionPerformed(e);
374 hydrophobicityColour.setText("By hydrophobicity");
375 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
377 public void actionPerformed(ActionEvent e)
379 hydrophobicityColour_actionPerformed(e);
382 helixColour.setText("Helix propensity");
383 helixColour.addActionListener(new java.awt.event.ActionListener()
385 public void actionPerformed(ActionEvent e)
387 helixColour_actionPerformed(e);
390 strandColour.setText("Strand propensity");
391 strandColour.addActionListener(new java.awt.event.ActionListener()
393 public void actionPerformed(ActionEvent e)
395 strandColour_actionPerformed(e);
398 turnColour.setText("Turn propensity");
399 turnColour.addActionListener(new java.awt.event.ActionListener()
401 public void actionPerformed(ActionEvent e)
403 turnColour_actionPerformed(e);
406 buriedColour.setText("Buried index");
407 buriedColour.addActionListener(new java.awt.event.ActionListener()
409 public void actionPerformed(ActionEvent e)
411 buriedColour_actionPerformed(e);
414 userDefinedColour.setText("User defined colours");
415 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
417 public void actionPerformed(ActionEvent e)
419 userDefinedColour_actionPerformed(e);
422 PIDColour.setText("Percentage Identity");
423 PIDColour.addActionListener(new java.awt.event.ActionListener()
425 public void actionPerformed(ActionEvent e)
427 PIDColour_actionPerformed(e);
430 BLOSUM62Colour.setText("BLOSUM62 score");
431 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
433 public void actionPerformed(ActionEvent e)
435 BLOSUM62Colour_actionPerformed(e);
438 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
439 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
441 public void actionPerformed(ActionEvent e)
443 avTreeBlosumMenuItem_actionPerformed(e);
446 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
447 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
449 public void actionPerformed(ActionEvent e)
451 njTreeBlosumMenuItem_actionPerformed(e);
454 annotationPanelMenuItem.setActionCommand("");
455 annotationPanelMenuItem.setText("Annotation Panel");
456 annotationPanelMenuItem.setState(true);
457 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
459 public void actionPerformed(ActionEvent e)
461 annotationPanelMenuItem_actionPerformed(e);
464 colourTextMenuItem.setText("Colour text");
465 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
467 public void actionPerformed(ActionEvent e)
469 colourTextMenuItem_actionPerformed(e);
472 htmlMenuItem.setText("Output as HTML");
473 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
475 public void actionPerformed(ActionEvent e)
477 htmlMenuItem_actionPerformed(e);
480 overviewMenuItem.setText("Overview window");
481 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
483 public void actionPerformed(ActionEvent e)
485 overviewMenuItem_actionPerformed(e);
488 undoMenuItem.setEnabled(false);
489 undoMenuItem.setMnemonic('Z');
490 undoMenuItem.setText("Undo");
491 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
493 public void actionPerformed(ActionEvent e)
495 undoMenuItem_actionPerformed(e);
498 redoMenuItem.setEnabled(false);
499 redoMenuItem.setMnemonic('0');
500 redoMenuItem.setText("Redo");
501 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
503 public void actionPerformed(ActionEvent e)
505 redoMenuItem_actionPerformed(e);
508 conservationMenuItem.setText("By conservation");
509 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
511 public void actionPerformed(ActionEvent e)
513 conservationMenuItem_actionPerformed(e);
516 noColourmenuItem.setText("None");
517 noColourmenuItem.setSelected(true);
518 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
520 public void actionPerformed(ActionEvent e)
522 noColourmenuItem_actionPerformed(e);
525 wrapMenuItem.setText("Wrap alignment");
526 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
528 public void actionPerformed(ActionEvent e)
530 wrapMenuItem_actionPerformed(e);
533 printMenuItem.setText("Print");
534 printMenuItem.addActionListener(new java.awt.event.ActionListener()
536 public void actionPerformed(ActionEvent e)
538 printMenuItem_actionPerformed(e);
541 renderGapsMenuItem.setText("Render gaps");
542 renderGapsMenuItem.setState(true);
543 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
545 public void actionPerformed(ActionEvent e)
547 renderGapsMenuItem_actionPerformed(e);
550 findMenuItem.setText("Find");
551 findMenuItem.addActionListener(new java.awt.event.ActionListener()
553 public void actionPerformed(ActionEvent e)
555 findMenuItem_actionPerformed(e);
558 searchMenu.setText("Search");
560 abovePIDThreshold.setText("Above PID threshold");
561 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
562 public void actionPerformed(ActionEvent e) {
563 abovePIDThreshold_actionPerformed(e);
566 sequenceFeatures.setText("Sequence Features");
567 sequenceFeatures.addActionListener(new ActionListener()
569 public void actionPerformed(ActionEvent actionEvent)
571 sequenceFeatures_actionPerformed(actionEvent);
574 nucleotideColour.setText("Nucleotide colours");
575 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
577 public void actionPerformed(ActionEvent e)
579 nucleotideColour_actionPerformed(e);
582 deleteGroups.setSelected(false);
583 deleteGroups.setText("Delete all groups");
584 deleteGroups.addActionListener(new java.awt.event.ActionListener()
586 public void actionPerformed(ActionEvent e)
588 deleteGroups_actionPerformed(e);
591 copy.setText("Copy");
592 copy.setMnemonic(KeyEvent.VK_C);
594 copy.addActionListener(new java.awt.event.ActionListener()
596 public void actionPerformed(ActionEvent e)
598 copy_actionPerformed(e);
602 cut.setMnemonic(KeyEvent.VK_X);
603 cut.addActionListener(new java.awt.event.ActionListener()
605 public void actionPerformed(ActionEvent e)
607 cut_actionPerformed(e);
610 delete.setText("Delete");
611 delete.addActionListener(new java.awt.event.ActionListener()
613 public void actionPerformed(ActionEvent e)
615 delete_actionPerformed(e);
618 jMenu1.setMnemonic('V');
619 jMenu1.setText("Paste");
620 pasteNew.setText("to new alignment");
621 pasteNew.addActionListener(new java.awt.event.ActionListener()
623 public void actionPerformed(ActionEvent e)
625 pasteNew_actionPerformed(e);
628 pasteThis.setText("add to this alignment");
629 pasteThis.addActionListener(new java.awt.event.ActionListener()
631 public void actionPerformed(ActionEvent e)
633 pasteThis_actionPerformed(e);
636 applyToAllGroups.setText("Apply colour to all groups");
637 applyToAllGroups.setState(true);
638 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
640 public void actionPerformed(ActionEvent e)
642 applyToAllGroups_actionPerformed(e);
645 createPNG.addActionListener(new java.awt.event.ActionListener()
647 public void actionPerformed(ActionEvent e)
649 createPNG_actionPerformed(e);
652 createPNG.setActionCommand("Save as PNG Image");
653 createPNG.setText("Save as PNG Image");
654 font.setText("Change Font");
655 font.addActionListener(new java.awt.event.ActionListener()
657 public void actionPerformed(ActionEvent e)
659 font_actionPerformed(e);
662 fullSeqId.setText("Show full sequence id");
663 fullSeqId.addActionListener(new java.awt.event.ActionListener()
665 public void actionPerformed(ActionEvent e)
667 fullSeqId_actionPerformed(e);
670 epsFile.setText("Save as EPS file");
671 epsFile.addActionListener(new java.awt.event.ActionListener()
673 public void actionPerformed(ActionEvent e)
675 epsFile_actionPerformed(e);
678 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
679 LoadtreeMenuItem.setText("Load assocated tree");
680 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
681 public void actionPerformed(ActionEvent e)
683 LoadtreeMenuItem_actionPerformed(e);
686 jpred.setText("JPred");
687 jpred.addActionListener(new java.awt.event.ActionListener()
689 public void actionPerformed(ActionEvent e)
691 jpred_actionPerformed(e);
694 scaleAbove.setVisible(false);
695 scaleAbove.setText("Scale above alignment");
696 scaleAbove.addActionListener(new java.awt.event.ActionListener()
698 public void actionPerformed(ActionEvent e)
700 scaleAbove_actionPerformed(e);
703 scaleLeft.setVisible(false);
704 scaleLeft.setSelected(true);
705 scaleLeft.setText("Scale left of sequence");
706 scaleLeft.addActionListener(new java.awt.event.ActionListener()
708 public void actionPerformed(ActionEvent e)
710 scaleLeft_actionPerformed(e);
713 scaleRight.setVisible(false);
714 scaleRight.setSelected(true);
715 scaleRight.setText("Scale right of sequence");
716 scaleRight.addActionListener(new java.awt.event.ActionListener()
718 public void actionPerformed(ActionEvent e)
720 scaleRight_actionPerformed(e);
723 alignFrameMenuBar.add(fileMenu);
724 alignFrameMenuBar.add(editMenu);
725 alignFrameMenuBar.add(searchMenu);
726 alignFrameMenuBar.add(viewMenu);
727 alignFrameMenuBar.add(colourMenu);
728 alignFrameMenuBar.add(calculateMenu);
729 alignFrameMenuBar.add(alignMenu);
730 fileMenu.add(saveAlignmentMenu);
731 fileMenu.add(outputTextboxMenu);
732 fileMenu.add(htmlMenuItem);
733 fileMenu.add(epsFile);
734 fileMenu.add(createPNG);
735 fileMenu.add(printMenuItem);
736 fileMenu.addSeparator();
737 fileMenu.add(LoadtreeMenuItem);
738 fileMenu.addSeparator();
739 fileMenu.add(closeMenuItem);
741 editMenu.add(jMenu1);
743 editMenu.add(delete);
744 editMenu.addSeparator();
745 editMenu.add(undoMenuItem);
746 editMenu.add(redoMenuItem);
747 editMenu.addSeparator();
748 editMenu.add(deselectAllSequenceMenuItem);
749 editMenu.add(selectAllSequenceMenuItem);
750 editMenu.add(invertSequenceMenuItem);
751 editMenu.add(deleteGroups);
752 editMenu.addSeparator();
753 editMenu.add(deselectAllColumnsMenuItem);
754 editMenu.add(remove2LeftMenuItem);
755 editMenu.add(remove2RightMenuItem);
756 editMenu.addSeparator();
757 editMenu.add(removeGappedColumnMenuItem);
758 editMenu.add(removeAllGapsMenuItem);
759 editMenu.add(setGapCharMenuItem);
760 searchMenu.add(findMenuItem);
762 viewMenu.add(fullSeqId);
763 viewMenu.addSeparator();
764 viewMenu.add(wrapMenuItem);
765 viewMenu.add(scaleAbove);
766 viewMenu.add(scaleLeft);
767 viewMenu.add(scaleRight);
768 viewMenu.addSeparator();
769 viewMenu.add(viewBoxesMenuItem);
770 viewMenu.add(viewTextMenuItem);
771 viewMenu.add(colourTextMenuItem);
772 viewMenu.add(renderGapsMenuItem);
773 viewMenu.add(annotationPanelMenuItem);
774 viewMenu.add(overviewMenuItem);
775 viewMenu.add(sequenceFeatures);
776 colourMenu.add(applyToAllGroups);
777 colourMenu.add(noColourmenuItem);
778 colourMenu.add(clustalColour);
779 colourMenu.add(zappoColour);
780 colourMenu.add(taylorColour);
781 colourMenu.add(hydrophobicityColour);
782 colourMenu.add(helixColour);
783 colourMenu.add(strandColour);
784 colourMenu.add(turnColour);
785 colourMenu.add(buriedColour);
786 colourMenu.add(nucleotideColour);
787 colourMenu.add(userDefinedColour);
788 colourMenu.add(PIDColour);
789 colourMenu.add(BLOSUM62Colour);
790 colourMenu.addSeparator();
791 colourMenu.add(abovePIDThreshold);
792 colourMenu.add(conservationMenuItem);
793 calculateMenu.add(sortPairwiseMenuItem);
794 calculateMenu.add(sortIDMenuItem);
795 calculateMenu.add(sortGroupMenuItem);
796 calculateMenu.add(sortTreeOrderMenuItem);
797 calculateMenu.add(removeRedundancyMenuItem);
798 calculateMenu.addSeparator();
799 calculateMenu.add(pairwiseAlignmentMenuItem);
800 calculateMenu.add(PCAMenuItem);
801 calculateMenu.addSeparator();
802 calculateMenu.add(averageDistanceTreeMenuItem);
803 calculateMenu.add(neighbourTreeMenuItem);
804 calculateMenu.add(avDistanceTreeBlosumMenuItem);
805 calculateMenu.add(njTreeBlosumMenuItem);
806 alignMenu.add(clustalAlignMenuItem);
807 alignMenu.add(jpred);
808 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
809 jMenu1.add(pasteNew);
810 jMenu1.add(pasteThis);
813 protected void saveAs_actionPerformed(ActionEvent e)
818 protected void outputText_actionPerformed(ActionEvent e)
823 protected void htmlMenuItem_actionPerformed(ActionEvent e)
832 protected void closeMenuItem_actionPerformed(ActionEvent e)
837 protected void redoMenuItem_actionPerformed(ActionEvent e)
842 protected void undoMenuItem_actionPerformed(ActionEvent e)
850 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
855 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
860 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
866 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
871 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
876 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
881 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
886 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
891 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
900 protected void wrapMenuItem_actionPerformed(ActionEvent e)
906 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
911 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
917 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
924 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
929 protected void overviewMenuItem_actionPerformed(ActionEvent e)
934 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
939 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
944 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
949 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
954 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
959 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
964 protected void PCAMenuItem_actionPerformed(ActionEvent e)
969 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
974 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
980 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
985 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
992 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
1000 protected void clustalColour_actionPerformed(ActionEvent e)
1005 protected void zappoColour_actionPerformed(ActionEvent e)
1010 protected void taylorColour_actionPerformed(ActionEvent e)
1016 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1021 protected void helixColour_actionPerformed(ActionEvent e)
1026 protected void strandColour_actionPerformed(ActionEvent e)
1031 protected void turnColour_actionPerformed(ActionEvent e)
1036 protected void buriedColour_actionPerformed(ActionEvent e)
1043 protected void userDefinedColour_actionPerformed(ActionEvent e)
1048 protected void PIDColour_actionPerformed(ActionEvent e)
1053 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1059 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1064 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1070 protected void printMenuItem_actionPerformed(ActionEvent e)
1075 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1080 protected void findMenuItem_actionPerformed(ActionEvent e)
1086 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
1090 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
1095 protected void nucleotideColour_actionPerformed(ActionEvent e)
1100 protected void deleteGroups_actionPerformed(ActionEvent e)
1105 protected void copy_actionPerformed(ActionEvent e)
1111 protected void cut_actionPerformed(ActionEvent e)
1116 protected void delete_actionPerformed(ActionEvent e)
1121 protected void pasteNew_actionPerformed(ActionEvent e)
1126 protected void pasteThis_actionPerformed(ActionEvent e)
1131 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1136 protected void createPNG_actionPerformed(ActionEvent e)
1141 protected void font_actionPerformed(ActionEvent e)
1146 protected void fullSeqId_actionPerformed(ActionEvent e)
1151 protected void epsFile_actionPerformed(ActionEvent e)
1156 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1160 protected void jpred_actionPerformed(ActionEvent e)
1165 protected void scaleAbove_actionPerformed(ActionEvent e)
1170 protected void scaleLeft_actionPerformed(ActionEvent e)
1175 protected void scaleRight_actionPerformed(ActionEvent e)