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();
100 JMenuItem msaAlignMenuItem = new JMenuItem();
108 setJMenuBar(alignFrameMenuBar);
111 // dynamically fill save as menu with available formats
112 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
113 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
114 saveAlignmentMenu.add( item );
115 item.addActionListener(new java.awt.event.ActionListener()
117 public void actionPerformed(ActionEvent e)
119 saveAs_actionPerformed(e);
123 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
124 item.addActionListener(new java.awt.event.ActionListener()
126 public void actionPerformed(ActionEvent e)
128 outputText_actionPerformed(e);
132 outputTextboxMenu.add( item );
141 ButtonGroup colours = new ButtonGroup();
142 colours.add(noColourmenuItem);
143 colours.add(clustalColour);
144 colours.add(zappoColour);
145 colours.add(taylorColour);
146 colours.add(hydrophobicityColour);
147 colours.add(helixColour);
148 colours.add(strandColour);
149 colours.add(turnColour);
150 colours.add(buriedColour);
151 colours.add(userDefinedColour);
152 colours.add(PIDColour);
153 colours.add(BLOSUM62Colour);
154 colours.add(nucleotideColour);
156 private void jbInit() throws Exception
158 fileMenu.setMnemonic('F');
159 fileMenu.setText("File");
160 saveAlignmentMenu.setMnemonic('L');
161 saveAlignmentMenu.setText("Save");
162 closeMenuItem.setMnemonic('C');
163 closeMenuItem.setText("Close");
164 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
166 public void actionPerformed(ActionEvent e)
168 closeMenuItem_actionPerformed(e);
171 editMenu.setText("Edit");
172 viewMenu.setText("View");
173 colourMenu.setText("Colour");
174 calculateMenu.setText("Calculate");
175 webService.setText("Web Service");
176 selectAllSequenceMenuItem.setText("Select all");
177 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
178 java.awt.event.KeyEvent.VK_A, java.awt.event.KeyEvent.CTRL_MASK, false));
179 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
181 public void actionPerformed(ActionEvent e)
183 selectAllSequenceMenuItem_actionPerformed(e);
186 deselectAllSequenceMenuItem.setText("Deselect All");
187 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
188 getKeyStroke(java.awt.event.
189 KeyEvent.VK_ESCAPE, 0, false));
190 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
192 public void actionPerformed(ActionEvent e)
194 deselectAllSequenceMenuItem_actionPerformed(e);
197 invertSequenceMenuItem.setText("Invert Selection");
198 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
200 public void actionPerformed(ActionEvent e)
202 invertSequenceMenuItem_actionPerformed(e);
205 remove2LeftMenuItem.setText("Remove Left");
206 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
208 public void actionPerformed(ActionEvent e)
210 remove2LeftMenuItem_actionPerformed(e);
213 remove2RightMenuItem.setText("Remove Right");
214 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
216 public void actionPerformed(ActionEvent e)
218 remove2RightMenuItem_actionPerformed(e);
221 removeGappedColumnMenuItem.setText("Remove Empty 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 viewBoxesMenuItem.setText("Boxes");
238 viewBoxesMenuItem.setState(true);
239 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
241 public void actionPerformed(ActionEvent e)
243 viewBoxesMenuItem_actionPerformed(e);
246 viewTextMenuItem.setText("Text");
247 viewTextMenuItem.setState(true);
248 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
250 public void actionPerformed(ActionEvent e)
252 viewTextMenuItem_actionPerformed(e);
255 sortPairwiseMenuItem.setText("Pairwise Identity");
256 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
258 public void actionPerformed(ActionEvent e)
260 sortPairwiseMenuItem_actionPerformed(e);
263 sortIDMenuItem.setText("ID");
264 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
266 public void actionPerformed(ActionEvent e)
268 sortIDMenuItem_actionPerformed(e);
271 sortGroupMenuItem.setText("Group");
272 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
274 public void actionPerformed(ActionEvent e)
276 sortGroupMenuItem_actionPerformed(e);
279 removeRedundancyMenuItem.setText("Remove Redundancy...");
280 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
282 public void actionPerformed(ActionEvent e)
284 removeRedundancyMenuItem_actionPerformed(e);
287 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
288 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
290 public void actionPerformed(ActionEvent e)
292 pairwiseAlignmentMenuItem_actionPerformed(e);
295 PCAMenuItem.setText("Principal Component Analysis...");
296 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
298 public void actionPerformed(ActionEvent e)
300 PCAMenuItem_actionPerformed(e);
303 averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
304 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
306 public void actionPerformed(ActionEvent e)
308 averageDistanceTreeMenuItem_actionPerformed(e);
311 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
312 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
314 public void actionPerformed(ActionEvent e)
316 neighbourTreeMenuItem_actionPerformed(e);
319 clustalAlignMenuItem.setText("Clustal Alignment...");
320 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
322 public void actionPerformed(ActionEvent e)
324 clustalAlignMenuItem_actionPerformed(e);
327 this.getContentPane().setLayout(borderLayout1);
328 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
329 statusBar.setBackground(Color.white);
330 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
331 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
332 statusBar.setText("Status bar");
333 outputTextboxMenu.setMnemonic('T');
334 outputTextboxMenu.setText("Output to Textbox");
335 clustalColour.setSelected(false);
336 clustalColour.setText("Clustalx");
337 clustalColour.addActionListener(new java.awt.event.ActionListener()
339 public void actionPerformed(ActionEvent e)
341 clustalColour_actionPerformed(e);
344 zappoColour.setText("Zappo");
345 zappoColour.addActionListener(new java.awt.event.ActionListener()
347 public void actionPerformed(ActionEvent e)
349 zappoColour_actionPerformed(e);
352 taylorColour.setText("Taylor");
353 taylorColour.addActionListener(new java.awt.event.ActionListener()
355 public void actionPerformed(ActionEvent e)
357 taylorColour_actionPerformed(e);
360 hydrophobicityColour.setText("Hydrophobicity");
361 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
363 public void actionPerformed(ActionEvent e)
365 hydrophobicityColour_actionPerformed(e);
368 helixColour.setText("Helix Propensity");
369 helixColour.addActionListener(new java.awt.event.ActionListener()
371 public void actionPerformed(ActionEvent e)
373 helixColour_actionPerformed(e);
376 strandColour.setText("Strand Propensity");
377 strandColour.addActionListener(new java.awt.event.ActionListener()
379 public void actionPerformed(ActionEvent e)
381 strandColour_actionPerformed(e);
384 turnColour.setText("Turn Propensity");
385 turnColour.addActionListener(new java.awt.event.ActionListener()
387 public void actionPerformed(ActionEvent e)
389 turnColour_actionPerformed(e);
392 buriedColour.setText("Buried Index");
393 buriedColour.addActionListener(new java.awt.event.ActionListener()
395 public void actionPerformed(ActionEvent e)
397 buriedColour_actionPerformed(e);
400 userDefinedColour.setText("User Defined...");
401 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
403 public void actionPerformed(ActionEvent e)
405 userDefinedColour_actionPerformed(e);
408 PIDColour.setText("Percentage Identity");
409 PIDColour.addActionListener(new java.awt.event.ActionListener()
411 public void actionPerformed(ActionEvent e)
413 PIDColour_actionPerformed(e);
416 BLOSUM62Colour.setText("BLOSUM62 Score");
417 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
419 public void actionPerformed(ActionEvent e)
421 BLOSUM62Colour_actionPerformed(e);
424 avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62...");
425 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
427 public void actionPerformed(ActionEvent e)
429 avTreeBlosumMenuItem_actionPerformed(e);
432 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
433 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
435 public void actionPerformed(ActionEvent e)
437 njTreeBlosumMenuItem_actionPerformed(e);
440 annotationPanelMenuItem.setActionCommand("");
441 annotationPanelMenuItem.setText("Show Annotations");
442 annotationPanelMenuItem.setState(true);
443 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
445 public void actionPerformed(ActionEvent e)
447 annotationPanelMenuItem_actionPerformed(e);
450 colourTextMenuItem.setText("Colour Text");
451 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
453 public void actionPerformed(ActionEvent e)
455 colourTextMenuItem_actionPerformed(e);
458 htmlMenuItem.setText("HTML");
459 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
461 public void actionPerformed(ActionEvent e)
463 htmlMenuItem_actionPerformed(e);
466 overviewMenuItem.setText("Overview Window...");
467 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
469 public void actionPerformed(ActionEvent e)
471 overviewMenuItem_actionPerformed(e);
474 undoMenuItem.setEnabled(false);
475 undoMenuItem.setMnemonic('Z');
476 undoMenuItem.setText("Undo");
477 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
478 event.KeyEvent.VK_Z, java.awt.event.KeyEvent.CTRL_MASK, false));
479 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
481 public void actionPerformed(ActionEvent e)
483 undoMenuItem_actionPerformed(e);
486 redoMenuItem.setEnabled(false);
487 redoMenuItem.setMnemonic('0');
488 redoMenuItem.setText("Redo");
489 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
491 public void actionPerformed(ActionEvent e)
493 redoMenuItem_actionPerformed(e);
496 conservationMenuItem.setText("By Conservation");
497 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
499 public void actionPerformed(ActionEvent e)
501 conservationMenuItem_actionPerformed(e);
504 noColourmenuItem.setText("None");
505 noColourmenuItem.setSelected(true);
506 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
508 public void actionPerformed(ActionEvent e)
510 noColourmenuItem_actionPerformed(e);
513 wrapMenuItem.setText("Wrap");
514 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
516 public void actionPerformed(ActionEvent e)
518 wrapMenuItem_actionPerformed(e);
521 printMenuItem.setText("Print");
522 printMenuItem.addActionListener(new java.awt.event.ActionListener()
524 public void actionPerformed(ActionEvent e)
526 printMenuItem_actionPerformed(e);
529 renderGapsMenuItem.setText("Show Gaps");
530 renderGapsMenuItem.setState(true);
531 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
533 public void actionPerformed(ActionEvent e)
535 renderGapsMenuItem_actionPerformed(e);
538 findMenuItem.setText("Find...");
539 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
540 event.KeyEvent.VK_F, java.awt.event.KeyEvent.CTRL_MASK, false));
541 findMenuItem.addActionListener(new java.awt.event.ActionListener()
543 public void actionPerformed(ActionEvent e)
545 findMenuItem_actionPerformed(e);
548 searchMenu.setText("Search");
550 abovePIDThreshold.setText("Above Identity threshold");
551 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
552 public void actionPerformed(ActionEvent e) {
553 abovePIDThreshold_actionPerformed(e);
556 sequenceFeatures.setText("Sequence Features");
557 sequenceFeatures.addActionListener(new ActionListener()
559 public void actionPerformed(ActionEvent actionEvent)
561 sequenceFeatures_actionPerformed(actionEvent);
564 nucleotideColour.setText("Nucleotide");
565 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
567 public void actionPerformed(ActionEvent e)
569 nucleotideColour_actionPerformed(e);
572 deleteGroups.setSelected(false);
573 deleteGroups.setText("Undefine groups");
574 deleteGroups.addActionListener(new java.awt.event.ActionListener()
576 public void actionPerformed(ActionEvent e)
578 deleteGroups_actionPerformed(e);
581 copy.setText("Copy");
582 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
583 KeyEvent.VK_C, java.awt.event.KeyEvent.CTRL_MASK, false));
584 copy.setMnemonic(KeyEvent.VK_C);
586 copy.addActionListener(new java.awt.event.ActionListener()
588 public void actionPerformed(ActionEvent e)
590 copy_actionPerformed(e);
594 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
595 KeyEvent.VK_X, java.awt.event.KeyEvent.CTRL_MASK, false));
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.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
616 KeyEvent.VK_V, java.awt.event.KeyEvent.CTRL_MASK, false));
617 pasteNew.addActionListener(new java.awt.event.ActionListener()
619 public void actionPerformed(ActionEvent e)
621 pasteNew_actionPerformed(e);
624 pasteThis.setText("add to this alignment");
625 pasteThis.addActionListener(new java.awt.event.ActionListener()
627 public void actionPerformed(ActionEvent e)
629 pasteThis_actionPerformed(e);
632 applyToAllGroups.setText("Apply Colour To All Groups");
633 applyToAllGroups.setState(true);
634 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
636 public void actionPerformed(ActionEvent e)
638 applyToAllGroups_actionPerformed(e);
641 createPNG.addActionListener(new java.awt.event.ActionListener()
643 public void actionPerformed(ActionEvent e)
645 createPNG_actionPerformed(e);
648 createPNG.setActionCommand("Save as PNG Image");
649 createPNG.setText("PNG");
650 font.setText("Font...");
651 font.addActionListener(new java.awt.event.ActionListener()
653 public void actionPerformed(ActionEvent e)
655 font_actionPerformed(e);
658 fullSeqId.setText("Show Full Sequence ID");
659 fullSeqId.addActionListener(new java.awt.event.ActionListener()
661 public void actionPerformed(ActionEvent e)
663 fullSeqId_actionPerformed(e);
666 epsFile.setText("EPS");
667 epsFile.addActionListener(new java.awt.event.ActionListener()
669 public void actionPerformed(ActionEvent e)
671 epsFile_actionPerformed(e);
674 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
675 LoadtreeMenuItem.setText("Load Assocated Tree");
676 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
677 public void actionPerformed(ActionEvent e)
679 LoadtreeMenuItem_actionPerformed(e);
682 jpred.setText("JPred...");
683 jpred.addActionListener(new java.awt.event.ActionListener()
685 public void actionPerformed(ActionEvent e)
687 jpred_actionPerformed(e);
690 scaleAbove.setVisible(false);
691 scaleAbove.setText("Scale Above");
692 scaleAbove.addActionListener(new java.awt.event.ActionListener()
694 public void actionPerformed(ActionEvent e)
696 scaleAbove_actionPerformed(e);
699 scaleLeft.setVisible(false);
700 scaleLeft.setSelected(true);
701 scaleLeft.setText("Scale Left");
702 scaleLeft.addActionListener(new java.awt.event.ActionListener()
704 public void actionPerformed(ActionEvent e)
706 scaleLeft_actionPerformed(e);
709 scaleRight.setVisible(false);
710 scaleRight.setSelected(true);
711 scaleRight.setText("Scale Right");
712 scaleRight.addActionListener(new java.awt.event.ActionListener()
714 public void actionPerformed(ActionEvent e)
716 scaleRight_actionPerformed(e);
719 modifyPID.setText("Modify Identity Threshold...");
720 modifyPID.addActionListener(new java.awt.event.ActionListener()
722 public void actionPerformed(ActionEvent e)
724 modifyPID_actionPerformed(e);
727 modifyConservation.setText("Modify Conservation Threshold...");
728 modifyConservation.addActionListener(new java.awt.event.ActionListener()
730 public void actionPerformed(ActionEvent e)
732 modifyConservation_actionPerformed(e);
735 sortByTreeMenu.setText("Tree Order");
736 jMenu2.setText("Save as");
737 sort.setText("Sort");
738 calculate.setText("Calculate Tree");
739 preferences.setText("Preferences...");
740 preferences.addActionListener(new ActionListener()
742 public void actionPerformed(ActionEvent e)
744 preferences_actionPerformed(e);
747 msaAlignMenuItem.setText("Muscle Alignment...");
748 msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
749 public void actionPerformed(ActionEvent e) {
750 msaAlignMenuItem_actionPerformed(e);
753 alignFrameMenuBar.add(fileMenu);
754 alignFrameMenuBar.add(editMenu);
755 alignFrameMenuBar.add(searchMenu);
756 alignFrameMenuBar.add(viewMenu);
757 alignFrameMenuBar.add(colourMenu);
758 alignFrameMenuBar.add(calculateMenu);
759 fileMenu.add(saveAlignmentMenu);
760 fileMenu.add(jMenu2);
761 fileMenu.add(outputTextboxMenu);
762 fileMenu.add(printMenuItem);
763 fileMenu.addSeparator();
764 fileMenu.add(LoadtreeMenuItem);
765 fileMenu.addSeparator();
766 fileMenu.add(closeMenuItem);
767 editMenu.add(undoMenuItem);
768 editMenu.add(redoMenuItem);
771 editMenu.add(jMenu1);
772 editMenu.add(delete);
773 editMenu.addSeparator();
774 editMenu.add(selectAllSequenceMenuItem);
775 editMenu.add(deselectAllSequenceMenuItem);
776 editMenu.add(invertSequenceMenuItem);
777 editMenu.add(deleteGroups);
778 editMenu.addSeparator();
779 editMenu.add(remove2LeftMenuItem);
780 editMenu.add(remove2RightMenuItem);
781 editMenu.add(removeGappedColumnMenuItem);
782 editMenu.add(removeAllGapsMenuItem);
783 editMenu.add(removeRedundancyMenuItem);
784 editMenu.addSeparator();
785 editMenu.add(preferences);
787 searchMenu.add(findMenuItem);
789 viewMenu.add(fullSeqId);
790 viewMenu.addSeparator();
791 viewMenu.add(wrapMenuItem);
792 viewMenu.add(scaleAbove);
793 viewMenu.add(scaleLeft);
794 viewMenu.add(scaleRight);
795 viewMenu.addSeparator();
796 viewMenu.add(viewBoxesMenuItem);
797 viewMenu.add(viewTextMenuItem);
798 viewMenu.add(colourTextMenuItem);
799 viewMenu.add(renderGapsMenuItem);
800 viewMenu.add(annotationPanelMenuItem);
801 viewMenu.add(sequenceFeatures);
802 viewMenu.addSeparator();
803 viewMenu.add(overviewMenuItem);
804 colourMenu.add(applyToAllGroups);
805 colourMenu.add(noColourmenuItem);
806 colourMenu.addSeparator();
807 colourMenu.add(clustalColour);
808 colourMenu.add(BLOSUM62Colour);
809 colourMenu.add(PIDColour);
810 colourMenu.add(zappoColour);
811 colourMenu.add(taylorColour);
812 colourMenu.add(hydrophobicityColour);
813 colourMenu.add(helixColour);
814 colourMenu.add(strandColour);
815 colourMenu.add(turnColour);
816 colourMenu.add(buriedColour);
817 colourMenu.add(nucleotideColour);
818 colourMenu.add(userDefinedColour);
819 colourMenu.addSeparator();
820 colourMenu.add(conservationMenuItem);
821 colourMenu.add(modifyConservation);
822 colourMenu.add(abovePIDThreshold);
823 colourMenu.add(modifyPID);
824 calculateMenu.add(sort);
825 calculateMenu.add(calculate);
826 calculateMenu.addSeparator();
827 calculateMenu.add(pairwiseAlignmentMenuItem);
828 calculateMenu.add(PCAMenuItem);
829 calculateMenu.addSeparator();
830 calculateMenu.add(webService);
831 webService.add(clustalAlignMenuItem);
832 webService.add(jpred);
833 webService.add(msaAlignMenuItem);
834 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
835 jMenu1.add(pasteNew);
836 jMenu1.add(pasteThis);
837 jMenu2.add(htmlMenuItem);
839 jMenu2.add(createPNG);
840 sort.add(sortIDMenuItem);
841 sort.add(sortGroupMenuItem);
842 sort.add(sortByTreeMenu);
843 sort.add(sortPairwiseMenuItem);
844 calculate.add(averageDistanceTreeMenuItem);
845 calculate.add(neighbourTreeMenuItem);
846 calculate.add(avDistanceTreeBlosumMenuItem);
847 calculate.add(njTreeBlosumMenuItem);
850 protected void saveAs_actionPerformed(ActionEvent e)
855 protected void outputText_actionPerformed(ActionEvent e)
860 protected void htmlMenuItem_actionPerformed(ActionEvent e)
866 protected void closeMenuItem_actionPerformed(ActionEvent e)
871 protected void redoMenuItem_actionPerformed(ActionEvent e)
876 protected void undoMenuItem_actionPerformed(ActionEvent e)
882 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
887 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
892 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
897 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
902 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
907 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
912 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
918 protected void wrapMenuItem_actionPerformed(ActionEvent e)
924 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
929 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
935 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
940 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
945 protected void overviewMenuItem_actionPerformed(ActionEvent e)
950 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
955 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
960 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
966 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
971 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
976 protected void PCAMenuItem_actionPerformed(ActionEvent e)
981 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
986 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
992 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
997 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1004 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
1012 protected void clustalColour_actionPerformed(ActionEvent e)
1017 protected void zappoColour_actionPerformed(ActionEvent e)
1022 protected void taylorColour_actionPerformed(ActionEvent e)
1028 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1033 protected void helixColour_actionPerformed(ActionEvent e)
1038 protected void strandColour_actionPerformed(ActionEvent e)
1043 protected void turnColour_actionPerformed(ActionEvent e)
1048 protected void buriedColour_actionPerformed(ActionEvent e)
1055 protected void userDefinedColour_actionPerformed(ActionEvent e)
1060 protected void PIDColour_actionPerformed(ActionEvent e)
1065 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1071 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1076 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1082 protected void printMenuItem_actionPerformed(ActionEvent e)
1087 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1092 protected void findMenuItem_actionPerformed(ActionEvent e)
1098 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
1102 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
1107 protected void nucleotideColour_actionPerformed(ActionEvent e)
1112 protected void deleteGroups_actionPerformed(ActionEvent e)
1117 protected void copy_actionPerformed(ActionEvent e)
1123 protected void cut_actionPerformed(ActionEvent e)
1128 protected void delete_actionPerformed(ActionEvent e)
1133 protected void pasteNew_actionPerformed(ActionEvent e)
1138 protected void pasteThis_actionPerformed(ActionEvent e)
1143 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1148 protected void createPNG_actionPerformed(ActionEvent e)
1153 protected void font_actionPerformed(ActionEvent e)
1158 protected void fullSeqId_actionPerformed(ActionEvent e)
1163 protected void epsFile_actionPerformed(ActionEvent e)
1168 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1172 protected void jpred_actionPerformed(ActionEvent e)
1177 protected void scaleAbove_actionPerformed(ActionEvent e)
1182 protected void scaleLeft_actionPerformed(ActionEvent e)
1187 protected void scaleRight_actionPerformed(ActionEvent e)
1192 protected void modifyPID_actionPerformed(ActionEvent e)
1197 protected void modifyConservation_actionPerformed(ActionEvent e)
1202 protected void preferences_actionPerformed(ActionEvent e)
1207 protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {