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 removeRedundancyMenuItem = new JMenuItem();
40 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
41 protected JMenuItem PCAMenuItem = new JMenuItem();
42 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
43 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
44 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
45 BorderLayout borderLayout1 = new BorderLayout();
46 public JLabel statusBar = new JLabel();
47 protected JMenu saveAlignmentMenu = new JMenu();
48 protected JMenu outputTextboxMenu = new JMenu();
49 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
50 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
51 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
52 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
53 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
54 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
55 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
56 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
57 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
58 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
59 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
60 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
61 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
62 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
63 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
64 JMenuItem htmlMenuItem = new JMenuItem();
65 JMenuItem overviewMenuItem = new JMenuItem();
66 protected JMenuItem undoMenuItem = new JMenuItem();
67 protected JMenuItem redoMenuItem = new JMenuItem();
68 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
69 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
70 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
71 JMenuItem printMenuItem = new JMenuItem();
72 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
73 JMenuItem findMenuItem = new JMenuItem();
74 JMenu searchMenu = new JMenu();
75 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
76 protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
77 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
78 JMenuItem deleteGroups = new JMenuItem();
79 JMenuItem delete = new JMenuItem();
80 JMenuItem copy = new JMenuItem();
81 JMenuItem cut = new JMenuItem();
82 JMenu jMenu1 = new JMenu();
83 JMenuItem pasteNew = new JMenuItem();
84 JMenuItem pasteThis = new JMenuItem();
85 protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
86 JMenuItem createPNG = new JMenuItem();
87 protected JMenuItem font = new JMenuItem();
88 protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
89 JMenuItem epsFile = new JMenuItem();
90 JMenuItem LoadtreeMenuItem = new JMenuItem();
91 JMenuItem jpred = new JMenuItem();
92 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
93 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
94 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
95 JMenuItem modifyPID = new JMenuItem();
96 JMenuItem modifyConservation = new JMenuItem();
97 protected JMenu sortByTreeMenu = new JMenu();
105 setJMenuBar(alignFrameMenuBar);
108 // dynamically fill save as menu with available formats
109 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
110 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
111 saveAlignmentMenu.add( item );
112 item.addActionListener(new java.awt.event.ActionListener()
114 public void actionPerformed(ActionEvent e)
116 saveAs_actionPerformed(e);
120 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
121 item.addActionListener(new java.awt.event.ActionListener()
123 public void actionPerformed(ActionEvent e)
125 outputText_actionPerformed(e);
129 outputTextboxMenu.add( item );
138 ButtonGroup colours = new ButtonGroup();
139 colours.add(noColourmenuItem);
140 colours.add(clustalColour);
141 colours.add(zappoColour);
142 colours.add(taylorColour);
143 colours.add(hydrophobicityColour);
144 colours.add(helixColour);
145 colours.add(strandColour);
146 colours.add(turnColour);
147 colours.add(buriedColour);
148 colours.add(userDefinedColour);
149 colours.add(PIDColour);
150 colours.add(BLOSUM62Colour);
151 colours.add(nucleotideColour);
153 private void jbInit() throws Exception
155 fileMenu.setMnemonic('F');
156 fileMenu.setText("File");
157 saveAlignmentMenu.setMnemonic('L');
158 saveAlignmentMenu.setText("Save alignment to local file");
159 closeMenuItem.setMnemonic('C');
160 closeMenuItem.setText("Close");
161 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
163 public void actionPerformed(ActionEvent e)
165 closeMenuItem_actionPerformed(e);
168 editMenu.setText("Edit");
169 viewMenu.setText("View");
170 colourMenu.setText("Colour");
171 calculateMenu.setText("Calculate");
172 alignMenu.setText("Web Service");
173 selectAllSequenceMenuItem.setText("Select all");
174 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
176 public void actionPerformed(ActionEvent e)
178 selectAllSequenceMenuItem_actionPerformed(e);
181 deselectAllSequenceMenuItem.setText("Clear selection");
182 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
184 public void actionPerformed(ActionEvent e)
186 deselectAllSequenceMenuItem_actionPerformed(e);
189 invertSequenceMenuItem.setText("Invert sequence selection");
190 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
192 public void actionPerformed(ActionEvent e)
194 invertSequenceMenuItem_actionPerformed(e);
197 deselectAllColumnsMenuItem.setText("Deselect all columns");
198 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
200 public void actionPerformed(ActionEvent e)
202 deselectAllColumnsMenuItem_actionPerformed(e);
205 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
206 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
208 public void actionPerformed(ActionEvent e)
210 remove2LeftMenuItem_actionPerformed(e);
213 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
214 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
216 public void actionPerformed(ActionEvent e)
218 remove2RightMenuItem_actionPerformed(e);
221 removeGappedColumnMenuItem.setText("Remove gapped columns");
222 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
224 public void actionPerformed(ActionEvent e)
226 removeGappedColumnMenuItem_actionPerformed(e);
229 removeAllGapsMenuItem.setText("Remove all gaps");
230 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
232 public void actionPerformed(ActionEvent e)
234 removeAllGapsMenuItem_actionPerformed(e);
237 setGapCharMenuItem.setText("Set gap character to \".\"");
238 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
240 public void actionPerformed(ActionEvent e)
242 setGapCharMenuItem_actionPerformed(e);
245 viewBoxesMenuItem.setText("Boxes");
246 viewBoxesMenuItem.setState(true);
247 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
249 public void actionPerformed(ActionEvent e)
251 viewBoxesMenuItem_actionPerformed(e);
254 viewTextMenuItem.setText("Text");
255 viewTextMenuItem.setState(true);
256 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
258 public void actionPerformed(ActionEvent e)
260 viewTextMenuItem_actionPerformed(e);
263 sortPairwiseMenuItem.setText("Sort by pairwise identity");
264 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
266 public void actionPerformed(ActionEvent e)
268 sortPairwiseMenuItem_actionPerformed(e);
271 sortIDMenuItem.setText("Sort by ID");
272 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
274 public void actionPerformed(ActionEvent e)
276 sortIDMenuItem_actionPerformed(e);
279 sortGroupMenuItem.setText("Sort by group");
280 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
282 public void actionPerformed(ActionEvent e)
284 sortGroupMenuItem_actionPerformed(e);
287 removeRedundancyMenuItem.setText("Remove redundancy");
288 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
290 public void actionPerformed(ActionEvent e)
292 removeRedundancyMenuItem_actionPerformed(e);
295 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
296 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
298 public void actionPerformed(ActionEvent e)
300 pairwiseAlignmentMenuItem_actionPerformed(e);
303 PCAMenuItem.setText("Principal component analysis");
304 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
306 public void actionPerformed(ActionEvent e)
308 PCAMenuItem_actionPerformed(e);
311 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
312 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
314 public void actionPerformed(ActionEvent e)
316 averageDistanceTreeMenuItem_actionPerformed(e);
319 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
320 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
322 public void actionPerformed(ActionEvent e)
324 neighbourTreeMenuItem_actionPerformed(e);
327 clustalAlignMenuItem.setText("Clustal alignment");
328 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
330 public void actionPerformed(ActionEvent e)
332 clustalAlignMenuItem_actionPerformed(e);
335 this.getContentPane().setLayout(borderLayout1);
336 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
337 statusBar.setBackground(Color.white);
338 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
339 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
340 statusBar.setText("Status bar");
341 outputTextboxMenu.setMnemonic('T');
342 outputTextboxMenu.setText("Output alignment via textbox");
343 clustalColour.setSelected(false);
344 clustalColour.setText("Clustalx colours");
345 clustalColour.addActionListener(new java.awt.event.ActionListener()
347 public void actionPerformed(ActionEvent e)
349 clustalColour_actionPerformed(e);
352 zappoColour.setText("Zappo colour scheme");
353 zappoColour.addActionListener(new java.awt.event.ActionListener()
355 public void actionPerformed(ActionEvent e)
357 zappoColour_actionPerformed(e);
360 taylorColour.setText("Taylor colour scheme");
361 taylorColour.addActionListener(new java.awt.event.ActionListener()
363 public void actionPerformed(ActionEvent e)
365 taylorColour_actionPerformed(e);
368 hydrophobicityColour.setText("By hydrophobicity");
369 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
371 public void actionPerformed(ActionEvent e)
373 hydrophobicityColour_actionPerformed(e);
376 helixColour.setText("Helix propensity");
377 helixColour.addActionListener(new java.awt.event.ActionListener()
379 public void actionPerformed(ActionEvent e)
381 helixColour_actionPerformed(e);
384 strandColour.setText("Strand propensity");
385 strandColour.addActionListener(new java.awt.event.ActionListener()
387 public void actionPerformed(ActionEvent e)
389 strandColour_actionPerformed(e);
392 turnColour.setText("Turn propensity");
393 turnColour.addActionListener(new java.awt.event.ActionListener()
395 public void actionPerformed(ActionEvent e)
397 turnColour_actionPerformed(e);
400 buriedColour.setText("Buried index");
401 buriedColour.addActionListener(new java.awt.event.ActionListener()
403 public void actionPerformed(ActionEvent e)
405 buriedColour_actionPerformed(e);
408 userDefinedColour.setText("User defined colours");
409 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
411 public void actionPerformed(ActionEvent e)
413 userDefinedColour_actionPerformed(e);
416 PIDColour.setText("Percentage Identity");
417 PIDColour.addActionListener(new java.awt.event.ActionListener()
419 public void actionPerformed(ActionEvent e)
421 PIDColour_actionPerformed(e);
424 BLOSUM62Colour.setText("BLOSUM62 score");
425 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
427 public void actionPerformed(ActionEvent e)
429 BLOSUM62Colour_actionPerformed(e);
432 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
433 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
435 public void actionPerformed(ActionEvent e)
437 avTreeBlosumMenuItem_actionPerformed(e);
440 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
441 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
443 public void actionPerformed(ActionEvent e)
445 njTreeBlosumMenuItem_actionPerformed(e);
448 annotationPanelMenuItem.setActionCommand("");
449 annotationPanelMenuItem.setText("Annotation Panel");
450 annotationPanelMenuItem.setState(true);
451 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
453 public void actionPerformed(ActionEvent e)
455 annotationPanelMenuItem_actionPerformed(e);
458 colourTextMenuItem.setText("Colour text");
459 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
461 public void actionPerformed(ActionEvent e)
463 colourTextMenuItem_actionPerformed(e);
466 htmlMenuItem.setText("Output as HTML");
467 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
469 public void actionPerformed(ActionEvent e)
471 htmlMenuItem_actionPerformed(e);
474 overviewMenuItem.setText("Overview window");
475 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
477 public void actionPerformed(ActionEvent e)
479 overviewMenuItem_actionPerformed(e);
482 undoMenuItem.setEnabled(false);
483 undoMenuItem.setMnemonic('Z');
484 undoMenuItem.setText("Undo");
485 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
487 public void actionPerformed(ActionEvent e)
489 undoMenuItem_actionPerformed(e);
492 redoMenuItem.setEnabled(false);
493 redoMenuItem.setMnemonic('0');
494 redoMenuItem.setText("Redo");
495 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
497 public void actionPerformed(ActionEvent e)
499 redoMenuItem_actionPerformed(e);
502 conservationMenuItem.setText("By conservation");
503 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
505 public void actionPerformed(ActionEvent e)
507 conservationMenuItem_actionPerformed(e);
510 noColourmenuItem.setText("None");
511 noColourmenuItem.setSelected(true);
512 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
514 public void actionPerformed(ActionEvent e)
516 noColourmenuItem_actionPerformed(e);
519 wrapMenuItem.setText("Wrap alignment");
520 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
522 public void actionPerformed(ActionEvent e)
524 wrapMenuItem_actionPerformed(e);
527 printMenuItem.setText("Print");
528 printMenuItem.addActionListener(new java.awt.event.ActionListener()
530 public void actionPerformed(ActionEvent e)
532 printMenuItem_actionPerformed(e);
535 renderGapsMenuItem.setText("Render gaps");
536 renderGapsMenuItem.setState(true);
537 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
539 public void actionPerformed(ActionEvent e)
541 renderGapsMenuItem_actionPerformed(e);
544 findMenuItem.setText("Find");
545 findMenuItem.addActionListener(new java.awt.event.ActionListener()
547 public void actionPerformed(ActionEvent e)
549 findMenuItem_actionPerformed(e);
552 searchMenu.setText("Search");
554 abovePIDThreshold.setText("Above PID threshold");
555 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
556 public void actionPerformed(ActionEvent e) {
557 abovePIDThreshold_actionPerformed(e);
560 sequenceFeatures.setText("Sequence Features");
561 sequenceFeatures.addActionListener(new ActionListener()
563 public void actionPerformed(ActionEvent actionEvent)
565 sequenceFeatures_actionPerformed(actionEvent);
568 nucleotideColour.setText("Nucleotide colours");
569 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
571 public void actionPerformed(ActionEvent e)
573 nucleotideColour_actionPerformed(e);
576 deleteGroups.setSelected(false);
577 deleteGroups.setText("Delete all groups");
578 deleteGroups.addActionListener(new java.awt.event.ActionListener()
580 public void actionPerformed(ActionEvent e)
582 deleteGroups_actionPerformed(e);
585 copy.setText("Copy");
586 copy.setMnemonic(KeyEvent.VK_C);
588 copy.addActionListener(new java.awt.event.ActionListener()
590 public void actionPerformed(ActionEvent e)
592 copy_actionPerformed(e);
596 cut.setMnemonic(KeyEvent.VK_X);
597 cut.addActionListener(new java.awt.event.ActionListener()
599 public void actionPerformed(ActionEvent e)
601 cut_actionPerformed(e);
604 delete.setText("Delete");
605 delete.addActionListener(new java.awt.event.ActionListener()
607 public void actionPerformed(ActionEvent e)
609 delete_actionPerformed(e);
612 jMenu1.setMnemonic('V');
613 jMenu1.setText("Paste");
614 pasteNew.setText("to new alignment");
615 pasteNew.addActionListener(new java.awt.event.ActionListener()
617 public void actionPerformed(ActionEvent e)
619 pasteNew_actionPerformed(e);
622 pasteThis.setText("add to this alignment");
623 pasteThis.addActionListener(new java.awt.event.ActionListener()
625 public void actionPerformed(ActionEvent e)
627 pasteThis_actionPerformed(e);
630 applyToAllGroups.setText("Apply colour to all groups");
631 applyToAllGroups.setState(true);
632 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
634 public void actionPerformed(ActionEvent e)
636 applyToAllGroups_actionPerformed(e);
639 createPNG.addActionListener(new java.awt.event.ActionListener()
641 public void actionPerformed(ActionEvent e)
643 createPNG_actionPerformed(e);
646 createPNG.setActionCommand("Save as PNG Image");
647 createPNG.setText("Save as PNG Image");
648 font.setText("Change Font");
649 font.addActionListener(new java.awt.event.ActionListener()
651 public void actionPerformed(ActionEvent e)
653 font_actionPerformed(e);
656 fullSeqId.setText("Show full sequence id");
657 fullSeqId.addActionListener(new java.awt.event.ActionListener()
659 public void actionPerformed(ActionEvent e)
661 fullSeqId_actionPerformed(e);
664 epsFile.setText("Save as EPS file");
665 epsFile.addActionListener(new java.awt.event.ActionListener()
667 public void actionPerformed(ActionEvent e)
669 epsFile_actionPerformed(e);
672 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
673 LoadtreeMenuItem.setText("Load assocated tree");
674 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
675 public void actionPerformed(ActionEvent e)
677 LoadtreeMenuItem_actionPerformed(e);
680 jpred.setText("JPred");
681 jpred.addActionListener(new java.awt.event.ActionListener()
683 public void actionPerformed(ActionEvent e)
685 jpred_actionPerformed(e);
688 scaleAbove.setVisible(false);
689 scaleAbove.setText("Scale above alignment");
690 scaleAbove.addActionListener(new java.awt.event.ActionListener()
692 public void actionPerformed(ActionEvent e)
694 scaleAbove_actionPerformed(e);
697 scaleLeft.setVisible(false);
698 scaleLeft.setSelected(true);
699 scaleLeft.setText("Scale left of sequence");
700 scaleLeft.addActionListener(new java.awt.event.ActionListener()
702 public void actionPerformed(ActionEvent e)
704 scaleLeft_actionPerformed(e);
707 scaleRight.setVisible(false);
708 scaleRight.setSelected(true);
709 scaleRight.setText("Scale right of sequence");
710 scaleRight.addActionListener(new java.awt.event.ActionListener()
712 public void actionPerformed(ActionEvent e)
714 scaleRight_actionPerformed(e);
717 modifyPID.setText("Modify PID Threshold");
718 modifyPID.addActionListener(new java.awt.event.ActionListener()
720 public void actionPerformed(ActionEvent e)
722 modifyPID_actionPerformed(e);
725 modifyConservation.setText("Modify Conservation Threshold");
726 modifyConservation.addActionListener(new java.awt.event.ActionListener()
728 public void actionPerformed(ActionEvent e)
730 modifyConservation_actionPerformed(e);
733 sortByTreeMenu.setText("Sort by tree order");
734 alignFrameMenuBar.add(fileMenu);
735 alignFrameMenuBar.add(editMenu);
736 alignFrameMenuBar.add(searchMenu);
737 alignFrameMenuBar.add(viewMenu);
738 alignFrameMenuBar.add(colourMenu);
739 alignFrameMenuBar.add(calculateMenu);
740 alignFrameMenuBar.add(alignMenu);
741 fileMenu.add(saveAlignmentMenu);
742 fileMenu.add(outputTextboxMenu);
743 fileMenu.add(htmlMenuItem);
744 fileMenu.add(epsFile);
745 fileMenu.add(createPNG);
746 fileMenu.add(printMenuItem);
747 fileMenu.addSeparator();
748 fileMenu.add(LoadtreeMenuItem);
749 fileMenu.addSeparator();
750 fileMenu.add(closeMenuItem);
752 editMenu.add(jMenu1);
754 editMenu.add(delete);
755 editMenu.addSeparator();
756 editMenu.add(undoMenuItem);
757 editMenu.add(redoMenuItem);
758 editMenu.addSeparator();
759 editMenu.add(deselectAllSequenceMenuItem);
760 editMenu.add(selectAllSequenceMenuItem);
761 editMenu.add(invertSequenceMenuItem);
762 editMenu.add(deleteGroups);
763 editMenu.addSeparator();
764 editMenu.add(deselectAllColumnsMenuItem);
765 editMenu.add(remove2LeftMenuItem);
766 editMenu.add(remove2RightMenuItem);
767 editMenu.addSeparator();
768 editMenu.add(removeGappedColumnMenuItem);
769 editMenu.add(removeAllGapsMenuItem);
770 editMenu.add(setGapCharMenuItem);
771 searchMenu.add(findMenuItem);
773 viewMenu.add(fullSeqId);
774 viewMenu.addSeparator();
775 viewMenu.add(wrapMenuItem);
776 viewMenu.add(scaleAbove);
777 viewMenu.add(scaleLeft);
778 viewMenu.add(scaleRight);
779 viewMenu.addSeparator();
780 viewMenu.add(viewBoxesMenuItem);
781 viewMenu.add(viewTextMenuItem);
782 viewMenu.add(colourTextMenuItem);
783 viewMenu.add(renderGapsMenuItem);
784 viewMenu.add(annotationPanelMenuItem);
785 viewMenu.add(overviewMenuItem);
786 viewMenu.add(sequenceFeatures);
787 colourMenu.add(applyToAllGroups);
788 colourMenu.add(noColourmenuItem);
789 colourMenu.add(clustalColour);
790 colourMenu.add(zappoColour);
791 colourMenu.add(taylorColour);
792 colourMenu.add(hydrophobicityColour);
793 colourMenu.add(helixColour);
794 colourMenu.add(strandColour);
795 colourMenu.add(turnColour);
796 colourMenu.add(buriedColour);
797 colourMenu.add(nucleotideColour);
798 colourMenu.add(userDefinedColour);
799 colourMenu.add(PIDColour);
800 colourMenu.add(BLOSUM62Colour);
801 colourMenu.addSeparator();
802 colourMenu.add(conservationMenuItem);
803 colourMenu.add(modifyConservation);
804 colourMenu.add(abovePIDThreshold);
805 colourMenu.add(modifyPID);
806 calculateMenu.add(sortPairwiseMenuItem);
807 calculateMenu.add(sortIDMenuItem);
808 calculateMenu.add(sortGroupMenuItem);
809 calculateMenu.add(sortByTreeMenu);
810 calculateMenu.add(removeRedundancyMenuItem);
811 calculateMenu.addSeparator();
812 calculateMenu.add(pairwiseAlignmentMenuItem);
813 calculateMenu.add(PCAMenuItem);
814 calculateMenu.addSeparator();
815 calculateMenu.add(averageDistanceTreeMenuItem);
816 calculateMenu.add(neighbourTreeMenuItem);
817 calculateMenu.add(avDistanceTreeBlosumMenuItem);
818 calculateMenu.add(njTreeBlosumMenuItem);
819 alignMenu.add(clustalAlignMenuItem);
820 alignMenu.add(jpred);
821 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
822 jMenu1.add(pasteNew);
823 jMenu1.add(pasteThis);
826 protected void saveAs_actionPerformed(ActionEvent e)
831 protected void outputText_actionPerformed(ActionEvent e)
836 protected void htmlMenuItem_actionPerformed(ActionEvent e)
845 protected void closeMenuItem_actionPerformed(ActionEvent e)
850 protected void redoMenuItem_actionPerformed(ActionEvent e)
855 protected void undoMenuItem_actionPerformed(ActionEvent e)
863 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
868 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
873 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
879 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
884 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
889 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
894 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
899 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
904 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
913 protected void wrapMenuItem_actionPerformed(ActionEvent e)
919 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
924 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
930 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
937 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
942 protected void overviewMenuItem_actionPerformed(ActionEvent e)
947 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
952 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
957 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
963 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
968 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
973 protected void PCAMenuItem_actionPerformed(ActionEvent e)
978 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
983 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
989 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
994 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1001 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
1009 protected void clustalColour_actionPerformed(ActionEvent e)
1014 protected void zappoColour_actionPerformed(ActionEvent e)
1019 protected void taylorColour_actionPerformed(ActionEvent e)
1025 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1030 protected void helixColour_actionPerformed(ActionEvent e)
1035 protected void strandColour_actionPerformed(ActionEvent e)
1040 protected void turnColour_actionPerformed(ActionEvent e)
1045 protected void buriedColour_actionPerformed(ActionEvent e)
1052 protected void userDefinedColour_actionPerformed(ActionEvent e)
1057 protected void PIDColour_actionPerformed(ActionEvent e)
1062 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1068 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1073 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1079 protected void printMenuItem_actionPerformed(ActionEvent e)
1084 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1089 protected void findMenuItem_actionPerformed(ActionEvent e)
1095 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
1099 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
1104 protected void nucleotideColour_actionPerformed(ActionEvent e)
1109 protected void deleteGroups_actionPerformed(ActionEvent e)
1114 protected void copy_actionPerformed(ActionEvent e)
1120 protected void cut_actionPerformed(ActionEvent e)
1125 protected void delete_actionPerformed(ActionEvent e)
1130 protected void pasteNew_actionPerformed(ActionEvent e)
1135 protected void pasteThis_actionPerformed(ActionEvent e)
1140 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1145 protected void createPNG_actionPerformed(ActionEvent e)
1150 protected void font_actionPerformed(ActionEvent e)
1155 protected void fullSeqId_actionPerformed(ActionEvent e)
1160 protected void epsFile_actionPerformed(ActionEvent e)
1165 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1169 protected void jpred_actionPerformed(ActionEvent e)
1174 protected void scaleAbove_actionPerformed(ActionEvent e)
1179 protected void scaleLeft_actionPerformed(ActionEvent e)
1184 protected void scaleRight_actionPerformed(ActionEvent e)
1189 protected void modifyPID_actionPerformed(ActionEvent e)
1194 protected void modifyConservation_actionPerformed(ActionEvent e)