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 webService = new JMenu();
25 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
26 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
27 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
28 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
29 protected JMenuItem remove2RightMenuItem = new JMenuItem();
30 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
31 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
32 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
33 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
34 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
35 protected JMenuItem sortIDMenuItem = new JMenuItem();
36 protected JMenuItem sortGroupMenuItem = new JMenuItem();
37 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
38 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
39 protected JMenuItem PCAMenuItem = new JMenuItem();
40 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
41 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
42 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
43 BorderLayout borderLayout1 = new BorderLayout();
44 public JLabel statusBar = new JLabel();
45 protected JMenu saveAlignmentMenu = new JMenu();
46 protected JMenu outputTextboxMenu = new JMenu();
47 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
48 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
49 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
50 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
51 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
52 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
53 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
54 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
55 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
56 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
57 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
58 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
59 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
60 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
61 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
62 JMenuItem htmlMenuItem = new JMenuItem();
63 JMenuItem overviewMenuItem = new JMenuItem();
64 protected JMenuItem undoMenuItem = new JMenuItem();
65 protected JMenuItem redoMenuItem = new JMenuItem();
66 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
67 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
68 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
69 JMenuItem printMenuItem = new JMenuItem();
70 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
71 JMenuItem findMenuItem = new JMenuItem();
72 JMenu searchMenu = new JMenu();
73 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
74 protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
75 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
76 JMenuItem deleteGroups = new JMenuItem();
77 JMenuItem delete = new JMenuItem();
78 JMenuItem copy = new JMenuItem();
79 JMenuItem cut = new JMenuItem();
80 JMenu jMenu1 = new JMenu();
81 JMenuItem pasteNew = new JMenuItem();
82 JMenuItem pasteThis = new JMenuItem();
83 protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
84 JMenuItem createPNG = new JMenuItem();
85 protected JMenuItem font = new JMenuItem();
86 protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
87 JMenuItem epsFile = new JMenuItem();
88 JMenuItem LoadtreeMenuItem = new JMenuItem();
89 JMenuItem jpred = new JMenuItem();
90 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
91 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
92 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
93 JMenuItem modifyPID = new JMenuItem();
94 JMenuItem modifyConservation = new JMenuItem();
95 protected JMenu sortByTreeMenu = new JMenu();
96 JMenu jMenu2 = new JMenu();
97 JMenu sort = new JMenu();
98 JMenu calculate = new JMenu();
99 JMenuItem preferences = new JMenuItem();
107 setJMenuBar(alignFrameMenuBar);
110 // dynamically fill save as menu with available formats
111 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
112 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
113 saveAlignmentMenu.add( item );
114 item.addActionListener(new java.awt.event.ActionListener()
116 public void actionPerformed(ActionEvent e)
118 saveAs_actionPerformed(e);
122 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
123 item.addActionListener(new java.awt.event.ActionListener()
125 public void actionPerformed(ActionEvent e)
127 outputText_actionPerformed(e);
131 outputTextboxMenu.add( item );
140 ButtonGroup colours = new ButtonGroup();
141 colours.add(noColourmenuItem);
142 colours.add(clustalColour);
143 colours.add(zappoColour);
144 colours.add(taylorColour);
145 colours.add(hydrophobicityColour);
146 colours.add(helixColour);
147 colours.add(strandColour);
148 colours.add(turnColour);
149 colours.add(buriedColour);
150 colours.add(userDefinedColour);
151 colours.add(PIDColour);
152 colours.add(BLOSUM62Colour);
153 colours.add(nucleotideColour);
155 private void jbInit() throws Exception
157 fileMenu.setMnemonic('F');
158 fileMenu.setText("File");
159 saveAlignmentMenu.setMnemonic('L');
160 saveAlignmentMenu.setText("Save");
161 closeMenuItem.setMnemonic('C');
162 closeMenuItem.setText("Close");
163 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
165 public void actionPerformed(ActionEvent e)
167 closeMenuItem_actionPerformed(e);
170 editMenu.setText("Edit");
171 viewMenu.setText("View");
172 colourMenu.setText("Colour");
173 calculateMenu.setText("Calculate");
174 webService.setText("Web Service");
175 selectAllSequenceMenuItem.setText("Select all");
176 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
177 java.awt.event.KeyEvent.VK_A, java.awt.event.KeyEvent.CTRL_MASK, false));
178 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
180 public void actionPerformed(ActionEvent e)
182 selectAllSequenceMenuItem_actionPerformed(e);
185 deselectAllSequenceMenuItem.setText("Deselect All");
186 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
187 getKeyStroke(java.awt.event.
188 KeyEvent.VK_ESCAPE, 0, false));
189 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
191 public void actionPerformed(ActionEvent e)
193 deselectAllSequenceMenuItem_actionPerformed(e);
196 invertSequenceMenuItem.setText("Invert Selection");
197 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
199 public void actionPerformed(ActionEvent e)
201 invertSequenceMenuItem_actionPerformed(e);
204 remove2LeftMenuItem.setText("Remove Left");
205 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
207 public void actionPerformed(ActionEvent e)
209 remove2LeftMenuItem_actionPerformed(e);
212 remove2RightMenuItem.setText("Remove Right");
213 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
215 public void actionPerformed(ActionEvent e)
217 remove2RightMenuItem_actionPerformed(e);
220 removeGappedColumnMenuItem.setText("Remove Empty Columns");
221 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
223 public void actionPerformed(ActionEvent e)
225 removeGappedColumnMenuItem_actionPerformed(e);
228 removeAllGapsMenuItem.setText("Remove All Gaps");
229 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
231 public void actionPerformed(ActionEvent e)
233 removeAllGapsMenuItem_actionPerformed(e);
236 viewBoxesMenuItem.setText("Boxes");
237 viewBoxesMenuItem.setState(true);
238 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
240 public void actionPerformed(ActionEvent e)
242 viewBoxesMenuItem_actionPerformed(e);
245 viewTextMenuItem.setText("Text");
246 viewTextMenuItem.setState(true);
247 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
249 public void actionPerformed(ActionEvent e)
251 viewTextMenuItem_actionPerformed(e);
254 sortPairwiseMenuItem.setText("Pairwise Identity");
255 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
257 public void actionPerformed(ActionEvent e)
259 sortPairwiseMenuItem_actionPerformed(e);
262 sortIDMenuItem.setText("ID");
263 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
265 public void actionPerformed(ActionEvent e)
267 sortIDMenuItem_actionPerformed(e);
270 sortGroupMenuItem.setText("Group");
271 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
273 public void actionPerformed(ActionEvent e)
275 sortGroupMenuItem_actionPerformed(e);
278 removeRedundancyMenuItem.setText("Remove Redundancy...");
279 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
281 public void actionPerformed(ActionEvent e)
283 removeRedundancyMenuItem_actionPerformed(e);
286 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
287 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
289 public void actionPerformed(ActionEvent e)
291 pairwiseAlignmentMenuItem_actionPerformed(e);
294 PCAMenuItem.setText("Principal Component Analysis...");
295 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
297 public void actionPerformed(ActionEvent e)
299 PCAMenuItem_actionPerformed(e);
302 averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
303 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
305 public void actionPerformed(ActionEvent e)
307 averageDistanceTreeMenuItem_actionPerformed(e);
310 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
311 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
313 public void actionPerformed(ActionEvent e)
315 neighbourTreeMenuItem_actionPerformed(e);
318 clustalAlignMenuItem.setText("Clustal Alignment...");
319 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
321 public void actionPerformed(ActionEvent e)
323 clustalAlignMenuItem_actionPerformed(e);
326 this.getContentPane().setLayout(borderLayout1);
327 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
328 statusBar.setBackground(Color.white);
329 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
330 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
331 statusBar.setText("Status bar");
332 outputTextboxMenu.setMnemonic('T');
333 outputTextboxMenu.setText("Output to Textbox");
334 clustalColour.setSelected(false);
335 clustalColour.setText("Clustalx");
336 clustalColour.addActionListener(new java.awt.event.ActionListener()
338 public void actionPerformed(ActionEvent e)
340 clustalColour_actionPerformed(e);
343 zappoColour.setText("Zappo");
344 zappoColour.addActionListener(new java.awt.event.ActionListener()
346 public void actionPerformed(ActionEvent e)
348 zappoColour_actionPerformed(e);
351 taylorColour.setText("Taylor");
352 taylorColour.addActionListener(new java.awt.event.ActionListener()
354 public void actionPerformed(ActionEvent e)
356 taylorColour_actionPerformed(e);
359 hydrophobicityColour.setText("Hydrophobicity");
360 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
362 public void actionPerformed(ActionEvent e)
364 hydrophobicityColour_actionPerformed(e);
367 helixColour.setText("Helix Propensity");
368 helixColour.addActionListener(new java.awt.event.ActionListener()
370 public void actionPerformed(ActionEvent e)
372 helixColour_actionPerformed(e);
375 strandColour.setText("Strand Propensity");
376 strandColour.addActionListener(new java.awt.event.ActionListener()
378 public void actionPerformed(ActionEvent e)
380 strandColour_actionPerformed(e);
383 turnColour.setText("Turn Propensity");
384 turnColour.addActionListener(new java.awt.event.ActionListener()
386 public void actionPerformed(ActionEvent e)
388 turnColour_actionPerformed(e);
391 buriedColour.setText("Buried Index");
392 buriedColour.addActionListener(new java.awt.event.ActionListener()
394 public void actionPerformed(ActionEvent e)
396 buriedColour_actionPerformed(e);
399 userDefinedColour.setText("User Defined...");
400 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
402 public void actionPerformed(ActionEvent e)
404 userDefinedColour_actionPerformed(e);
407 PIDColour.setText("Percentage Identity");
408 PIDColour.addActionListener(new java.awt.event.ActionListener()
410 public void actionPerformed(ActionEvent e)
412 PIDColour_actionPerformed(e);
415 BLOSUM62Colour.setText("BLOSUM62 Score");
416 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
418 public void actionPerformed(ActionEvent e)
420 BLOSUM62Colour_actionPerformed(e);
423 avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62...");
424 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
426 public void actionPerformed(ActionEvent e)
428 avTreeBlosumMenuItem_actionPerformed(e);
431 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
432 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
434 public void actionPerformed(ActionEvent e)
436 njTreeBlosumMenuItem_actionPerformed(e);
439 annotationPanelMenuItem.setActionCommand("");
440 annotationPanelMenuItem.setText("Show Annotations");
441 annotationPanelMenuItem.setState(true);
442 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
444 public void actionPerformed(ActionEvent e)
446 annotationPanelMenuItem_actionPerformed(e);
449 colourTextMenuItem.setText("Colour Text");
450 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
452 public void actionPerformed(ActionEvent e)
454 colourTextMenuItem_actionPerformed(e);
457 htmlMenuItem.setText("HTML");
458 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
460 public void actionPerformed(ActionEvent e)
462 htmlMenuItem_actionPerformed(e);
465 overviewMenuItem.setText("Overview Window...");
466 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
468 public void actionPerformed(ActionEvent e)
470 overviewMenuItem_actionPerformed(e);
473 undoMenuItem.setEnabled(false);
474 undoMenuItem.setMnemonic('Z');
475 undoMenuItem.setText("Undo");
476 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
477 event.KeyEvent.VK_Z, java.awt.event.KeyEvent.CTRL_MASK, false));
478 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
480 public void actionPerformed(ActionEvent e)
482 undoMenuItem_actionPerformed(e);
485 redoMenuItem.setEnabled(false);
486 redoMenuItem.setMnemonic('0');
487 redoMenuItem.setText("Redo");
488 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
490 public void actionPerformed(ActionEvent e)
492 redoMenuItem_actionPerformed(e);
495 conservationMenuItem.setText("By Conservation");
496 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
498 public void actionPerformed(ActionEvent e)
500 conservationMenuItem_actionPerformed(e);
503 noColourmenuItem.setText("None");
504 noColourmenuItem.setSelected(true);
505 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
507 public void actionPerformed(ActionEvent e)
509 noColourmenuItem_actionPerformed(e);
512 wrapMenuItem.setText("Wrap");
513 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
515 public void actionPerformed(ActionEvent e)
517 wrapMenuItem_actionPerformed(e);
520 printMenuItem.setText("Print");
521 printMenuItem.addActionListener(new java.awt.event.ActionListener()
523 public void actionPerformed(ActionEvent e)
525 printMenuItem_actionPerformed(e);
528 renderGapsMenuItem.setText("Show Gaps");
529 renderGapsMenuItem.setState(true);
530 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
532 public void actionPerformed(ActionEvent e)
534 renderGapsMenuItem_actionPerformed(e);
537 findMenuItem.setText("Find...");
538 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
539 event.KeyEvent.VK_F, java.awt.event.KeyEvent.CTRL_MASK, false));
540 findMenuItem.addActionListener(new java.awt.event.ActionListener()
542 public void actionPerformed(ActionEvent e)
544 findMenuItem_actionPerformed(e);
547 searchMenu.setText("Search");
549 abovePIDThreshold.setText("Above Identity threshold");
550 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
551 public void actionPerformed(ActionEvent e) {
552 abovePIDThreshold_actionPerformed(e);
555 sequenceFeatures.setText("Sequence Features");
556 sequenceFeatures.addActionListener(new ActionListener()
558 public void actionPerformed(ActionEvent actionEvent)
560 sequenceFeatures_actionPerformed(actionEvent);
563 nucleotideColour.setText("Nucleotide");
564 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
566 public void actionPerformed(ActionEvent e)
568 nucleotideColour_actionPerformed(e);
571 deleteGroups.setSelected(false);
572 deleteGroups.setText("Undefine groups");
573 deleteGroups.addActionListener(new java.awt.event.ActionListener()
575 public void actionPerformed(ActionEvent e)
577 deleteGroups_actionPerformed(e);
580 copy.setText("Copy");
581 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
582 KeyEvent.VK_C, java.awt.event.KeyEvent.CTRL_MASK, false));
583 copy.setMnemonic(KeyEvent.VK_C);
585 copy.addActionListener(new java.awt.event.ActionListener()
587 public void actionPerformed(ActionEvent e)
589 copy_actionPerformed(e);
593 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
594 KeyEvent.VK_X, java.awt.event.KeyEvent.CTRL_MASK, false));
595 cut.setMnemonic(KeyEvent.VK_X);
596 cut.addActionListener(new java.awt.event.ActionListener()
598 public void actionPerformed(ActionEvent e)
600 cut_actionPerformed(e);
603 delete.setText("Delete");
604 delete.addActionListener(new java.awt.event.ActionListener()
606 public void actionPerformed(ActionEvent e)
608 delete_actionPerformed(e);
611 jMenu1.setMnemonic('V');
612 jMenu1.setText("Paste");
613 pasteNew.setText("to new alignment");
614 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
615 KeyEvent.VK_V, java.awt.event.KeyEvent.CTRL_MASK, false));
616 pasteNew.addActionListener(new java.awt.event.ActionListener()
618 public void actionPerformed(ActionEvent e)
620 pasteNew_actionPerformed(e);
623 pasteThis.setText("add to this alignment");
624 pasteThis.addActionListener(new java.awt.event.ActionListener()
626 public void actionPerformed(ActionEvent e)
628 pasteThis_actionPerformed(e);
631 applyToAllGroups.setText("Apply Colour To All Groups");
632 applyToAllGroups.setState(true);
633 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
635 public void actionPerformed(ActionEvent e)
637 applyToAllGroups_actionPerformed(e);
640 createPNG.addActionListener(new java.awt.event.ActionListener()
642 public void actionPerformed(ActionEvent e)
644 createPNG_actionPerformed(e);
647 createPNG.setActionCommand("Save as PNG Image");
648 createPNG.setText("PNG");
649 font.setText("Font...");
650 font.addActionListener(new java.awt.event.ActionListener()
652 public void actionPerformed(ActionEvent e)
654 font_actionPerformed(e);
657 fullSeqId.setText("Show Full Sequence ID");
658 fullSeqId.addActionListener(new java.awt.event.ActionListener()
660 public void actionPerformed(ActionEvent e)
662 fullSeqId_actionPerformed(e);
665 epsFile.setText("EPS");
666 epsFile.addActionListener(new java.awt.event.ActionListener()
668 public void actionPerformed(ActionEvent e)
670 epsFile_actionPerformed(e);
673 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
674 LoadtreeMenuItem.setText("Load Assocated Tree");
675 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
676 public void actionPerformed(ActionEvent e)
678 LoadtreeMenuItem_actionPerformed(e);
681 jpred.setText("JPred...");
682 jpred.addActionListener(new java.awt.event.ActionListener()
684 public void actionPerformed(ActionEvent e)
686 jpred_actionPerformed(e);
689 scaleAbove.setVisible(false);
690 scaleAbove.setText("Scale Above");
691 scaleAbove.addActionListener(new java.awt.event.ActionListener()
693 public void actionPerformed(ActionEvent e)
695 scaleAbove_actionPerformed(e);
698 scaleLeft.setVisible(false);
699 scaleLeft.setSelected(true);
700 scaleLeft.setText("Scale Left");
701 scaleLeft.addActionListener(new java.awt.event.ActionListener()
703 public void actionPerformed(ActionEvent e)
705 scaleLeft_actionPerformed(e);
708 scaleRight.setVisible(false);
709 scaleRight.setSelected(true);
710 scaleRight.setText("Scale Right");
711 scaleRight.addActionListener(new java.awt.event.ActionListener()
713 public void actionPerformed(ActionEvent e)
715 scaleRight_actionPerformed(e);
718 modifyPID.setText("Modify Identity Threshold...");
719 modifyPID.addActionListener(new java.awt.event.ActionListener()
721 public void actionPerformed(ActionEvent e)
723 modifyPID_actionPerformed(e);
726 modifyConservation.setText("Modify Conservation Threshold...");
727 modifyConservation.addActionListener(new java.awt.event.ActionListener()
729 public void actionPerformed(ActionEvent e)
731 modifyConservation_actionPerformed(e);
734 sortByTreeMenu.setText("Tree Order");
735 jMenu2.setText("Save as");
736 sort.setText("Sort");
737 calculate.setText("Calculate Tree");
738 preferences.setText("Preferences...");
739 preferences.addActionListener(new ActionListener()
741 public void actionPerformed(ActionEvent e)
743 preferences_actionPerformed(e);
746 alignFrameMenuBar.add(fileMenu);
747 alignFrameMenuBar.add(editMenu);
748 alignFrameMenuBar.add(searchMenu);
749 alignFrameMenuBar.add(viewMenu);
750 alignFrameMenuBar.add(colourMenu);
751 alignFrameMenuBar.add(calculateMenu);
752 fileMenu.add(saveAlignmentMenu);
753 fileMenu.add(jMenu2);
754 fileMenu.add(outputTextboxMenu);
755 fileMenu.add(printMenuItem);
756 fileMenu.addSeparator();
757 fileMenu.add(LoadtreeMenuItem);
758 fileMenu.addSeparator();
759 fileMenu.add(closeMenuItem);
760 editMenu.add(undoMenuItem);
761 editMenu.add(redoMenuItem);
764 editMenu.add(jMenu1);
765 editMenu.add(delete);
766 editMenu.addSeparator();
767 editMenu.add(selectAllSequenceMenuItem);
768 editMenu.add(deselectAllSequenceMenuItem);
769 editMenu.add(invertSequenceMenuItem);
770 editMenu.add(deleteGroups);
771 editMenu.addSeparator();
772 editMenu.add(remove2LeftMenuItem);
773 editMenu.add(remove2RightMenuItem);
774 editMenu.add(removeGappedColumnMenuItem);
775 editMenu.add(removeAllGapsMenuItem);
776 editMenu.add(removeRedundancyMenuItem);
777 editMenu.addSeparator();
778 editMenu.add(preferences);
780 searchMenu.add(findMenuItem);
782 viewMenu.add(fullSeqId);
783 viewMenu.addSeparator();
784 viewMenu.add(wrapMenuItem);
785 viewMenu.add(scaleAbove);
786 viewMenu.add(scaleLeft);
787 viewMenu.add(scaleRight);
788 viewMenu.addSeparator();
789 viewMenu.add(viewBoxesMenuItem);
790 viewMenu.add(viewTextMenuItem);
791 viewMenu.add(colourTextMenuItem);
792 viewMenu.add(renderGapsMenuItem);
793 viewMenu.add(annotationPanelMenuItem);
794 viewMenu.add(sequenceFeatures);
795 viewMenu.addSeparator();
796 viewMenu.add(overviewMenuItem);
797 colourMenu.add(applyToAllGroups);
798 colourMenu.add(noColourmenuItem);
799 colourMenu.addSeparator();
800 colourMenu.add(clustalColour);
801 colourMenu.add(BLOSUM62Colour);
802 colourMenu.add(PIDColour);
803 colourMenu.add(zappoColour);
804 colourMenu.add(taylorColour);
805 colourMenu.add(hydrophobicityColour);
806 colourMenu.add(helixColour);
807 colourMenu.add(strandColour);
808 colourMenu.add(turnColour);
809 colourMenu.add(buriedColour);
810 colourMenu.add(nucleotideColour);
811 colourMenu.add(userDefinedColour);
812 colourMenu.addSeparator();
813 colourMenu.add(conservationMenuItem);
814 colourMenu.add(modifyConservation);
815 colourMenu.add(abovePIDThreshold);
816 colourMenu.add(modifyPID);
817 calculateMenu.add(sort);
818 calculateMenu.add(calculate);
819 calculateMenu.addSeparator();
820 calculateMenu.add(pairwiseAlignmentMenuItem);
821 calculateMenu.add(PCAMenuItem);
822 calculateMenu.addSeparator();
823 calculateMenu.add(webService);
824 webService.add(clustalAlignMenuItem);
825 webService.add(jpred);
826 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
827 jMenu1.add(pasteNew);
828 jMenu1.add(pasteThis);
829 jMenu2.add(htmlMenuItem);
831 jMenu2.add(createPNG);
832 sort.add(sortIDMenuItem);
833 sort.add(sortGroupMenuItem);
834 sort.add(sortByTreeMenu);
835 sort.add(sortPairwiseMenuItem);
836 calculate.add(averageDistanceTreeMenuItem);
837 calculate.add(neighbourTreeMenuItem);
838 calculate.add(avDistanceTreeBlosumMenuItem);
839 calculate.add(njTreeBlosumMenuItem);
842 protected void saveAs_actionPerformed(ActionEvent e)
847 protected void outputText_actionPerformed(ActionEvent e)
852 protected void htmlMenuItem_actionPerformed(ActionEvent e)
858 protected void closeMenuItem_actionPerformed(ActionEvent e)
863 protected void redoMenuItem_actionPerformed(ActionEvent e)
868 protected void undoMenuItem_actionPerformed(ActionEvent e)
874 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
879 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
884 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
889 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
894 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
899 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
904 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
910 protected void wrapMenuItem_actionPerformed(ActionEvent e)
916 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
921 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
927 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
932 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
937 protected void overviewMenuItem_actionPerformed(ActionEvent e)
942 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
947 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
952 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
958 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
963 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
968 protected void PCAMenuItem_actionPerformed(ActionEvent e)
973 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
978 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
984 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
989 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
996 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
1004 protected void clustalColour_actionPerformed(ActionEvent e)
1009 protected void zappoColour_actionPerformed(ActionEvent e)
1014 protected void taylorColour_actionPerformed(ActionEvent e)
1020 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1025 protected void helixColour_actionPerformed(ActionEvent e)
1030 protected void strandColour_actionPerformed(ActionEvent e)
1035 protected void turnColour_actionPerformed(ActionEvent e)
1040 protected void buriedColour_actionPerformed(ActionEvent e)
1047 protected void userDefinedColour_actionPerformed(ActionEvent e)
1052 protected void PIDColour_actionPerformed(ActionEvent e)
1057 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1063 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1068 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1074 protected void printMenuItem_actionPerformed(ActionEvent e)
1079 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1084 protected void findMenuItem_actionPerformed(ActionEvent e)
1090 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
1094 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
1099 protected void nucleotideColour_actionPerformed(ActionEvent e)
1104 protected void deleteGroups_actionPerformed(ActionEvent e)
1109 protected void copy_actionPerformed(ActionEvent e)
1115 protected void cut_actionPerformed(ActionEvent e)
1120 protected void delete_actionPerformed(ActionEvent e)
1125 protected void pasteNew_actionPerformed(ActionEvent e)
1130 protected void pasteThis_actionPerformed(ActionEvent e)
1135 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1140 protected void createPNG_actionPerformed(ActionEvent e)
1145 protected void font_actionPerformed(ActionEvent e)
1150 protected void fullSeqId_actionPerformed(ActionEvent e)
1155 protected void epsFile_actionPerformed(ActionEvent e)
1160 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1164 protected void jpred_actionPerformed(ActionEvent e)
1169 protected void scaleAbove_actionPerformed(ActionEvent e)
1174 protected void scaleLeft_actionPerformed(ActionEvent e)
1179 protected void scaleRight_actionPerformed(ActionEvent e)
1184 protected void modifyPID_actionPerformed(ActionEvent e)
1189 protected void modifyConservation_actionPerformed(ActionEvent e)
1194 protected void preferences_actionPerformed(ActionEvent e)