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 protected JMenuItem msaAlignMenuItem = 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();
96 JMenuItem modifyPID = new JMenuItem();
97 JMenuItem modifyConservation = new JMenuItem();
98 protected JMenu sortByTreeMenu = new JMenu();
106 setJMenuBar(alignFrameMenuBar);
109 // dynamically fill save as menu with available formats
110 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
111 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
112 saveAlignmentMenu.add( item );
113 item.addActionListener(new java.awt.event.ActionListener()
115 public void actionPerformed(ActionEvent e)
117 saveAs_actionPerformed(e);
121 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
122 item.addActionListener(new java.awt.event.ActionListener()
124 public void actionPerformed(ActionEvent e)
126 outputText_actionPerformed(e);
130 outputTextboxMenu.add( item );
139 ButtonGroup colours = new ButtonGroup();
140 colours.add(noColourmenuItem);
141 colours.add(clustalColour);
142 colours.add(zappoColour);
143 colours.add(taylorColour);
144 colours.add(hydrophobicityColour);
145 colours.add(helixColour);
146 colours.add(strandColour);
147 colours.add(turnColour);
148 colours.add(buriedColour);
149 colours.add(userDefinedColour);
150 colours.add(PIDColour);
151 colours.add(BLOSUM62Colour);
152 colours.add(nucleotideColour);
154 private void jbInit() throws Exception
156 fileMenu.setMnemonic('F');
157 fileMenu.setText("File");
158 saveAlignmentMenu.setMnemonic('L');
159 saveAlignmentMenu.setText("Save alignment to local file");
160 closeMenuItem.setMnemonic('C');
161 closeMenuItem.setText("Close");
162 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
164 public void actionPerformed(ActionEvent e)
166 closeMenuItem_actionPerformed(e);
169 editMenu.setText("Edit");
170 viewMenu.setText("View");
171 colourMenu.setText("Colour");
172 calculateMenu.setText("Calculate");
173 alignMenu.setText("Web Service");
174 selectAllSequenceMenuItem.setText("Select all");
175 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
177 public void actionPerformed(ActionEvent e)
179 selectAllSequenceMenuItem_actionPerformed(e);
182 deselectAllSequenceMenuItem.setText("Clear selection");
183 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
185 public void actionPerformed(ActionEvent e)
187 deselectAllSequenceMenuItem_actionPerformed(e);
190 invertSequenceMenuItem.setText("Invert sequence selection");
191 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
193 public void actionPerformed(ActionEvent e)
195 invertSequenceMenuItem_actionPerformed(e);
198 deselectAllColumnsMenuItem.setText("Deselect all columns");
199 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
201 public void actionPerformed(ActionEvent e)
203 deselectAllColumnsMenuItem_actionPerformed(e);
206 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
207 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
209 public void actionPerformed(ActionEvent e)
211 remove2LeftMenuItem_actionPerformed(e);
214 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
215 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
217 public void actionPerformed(ActionEvent e)
219 remove2RightMenuItem_actionPerformed(e);
222 removeGappedColumnMenuItem.setText("Remove gapped columns");
223 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
225 public void actionPerformed(ActionEvent e)
227 removeGappedColumnMenuItem_actionPerformed(e);
230 removeAllGapsMenuItem.setText("Remove all gaps");
231 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
233 public void actionPerformed(ActionEvent e)
235 removeAllGapsMenuItem_actionPerformed(e);
238 setGapCharMenuItem.setText("Set gap character to \".\"");
239 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
241 public void actionPerformed(ActionEvent e)
243 setGapCharMenuItem_actionPerformed(e);
246 viewBoxesMenuItem.setText("Boxes");
247 viewBoxesMenuItem.setState(true);
248 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
250 public void actionPerformed(ActionEvent e)
252 viewBoxesMenuItem_actionPerformed(e);
255 viewTextMenuItem.setText("Text");
256 viewTextMenuItem.setState(true);
257 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
259 public void actionPerformed(ActionEvent e)
261 viewTextMenuItem_actionPerformed(e);
264 sortPairwiseMenuItem.setText("Sort by pairwise identity");
265 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
267 public void actionPerformed(ActionEvent e)
269 sortPairwiseMenuItem_actionPerformed(e);
272 sortIDMenuItem.setText("Sort by ID");
273 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
275 public void actionPerformed(ActionEvent e)
277 sortIDMenuItem_actionPerformed(e);
280 sortGroupMenuItem.setText("Sort by group");
281 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
283 public void actionPerformed(ActionEvent e)
285 sortGroupMenuItem_actionPerformed(e);
288 removeRedundancyMenuItem.setText("Remove redundancy");
289 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
291 public void actionPerformed(ActionEvent e)
293 removeRedundancyMenuItem_actionPerformed(e);
296 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
297 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
299 public void actionPerformed(ActionEvent e)
301 pairwiseAlignmentMenuItem_actionPerformed(e);
304 PCAMenuItem.setText("Principal component analysis");
305 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
307 public void actionPerformed(ActionEvent e)
309 PCAMenuItem_actionPerformed(e);
312 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
313 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
315 public void actionPerformed(ActionEvent e)
317 averageDistanceTreeMenuItem_actionPerformed(e);
320 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
321 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
323 public void actionPerformed(ActionEvent e)
325 neighbourTreeMenuItem_actionPerformed(e);
328 clustalAlignMenuItem.setText("Clustal alignment");
329 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
331 public void actionPerformed(ActionEvent e)
333 clustalAlignMenuItem_actionPerformed(e);
336 msaAlignMenuItem.setText("Muscle alignment");
337 msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
339 public void actionPerformed(ActionEvent e)
341 msaAlignMenuItem_actionPerformed(e);
344 this.getContentPane().setLayout(borderLayout1);
345 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
346 statusBar.setBackground(Color.white);
347 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
348 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
349 statusBar.setText("Status bar");
350 outputTextboxMenu.setMnemonic('T');
351 outputTextboxMenu.setText("Output alignment via textbox");
352 clustalColour.setSelected(false);
353 clustalColour.setText("Clustalx colours");
354 clustalColour.addActionListener(new java.awt.event.ActionListener()
356 public void actionPerformed(ActionEvent e)
358 clustalColour_actionPerformed(e);
361 zappoColour.setText("Zappo colour scheme");
362 zappoColour.addActionListener(new java.awt.event.ActionListener()
364 public void actionPerformed(ActionEvent e)
366 zappoColour_actionPerformed(e);
369 taylorColour.setText("Taylor colour scheme");
370 taylorColour.addActionListener(new java.awt.event.ActionListener()
372 public void actionPerformed(ActionEvent e)
374 taylorColour_actionPerformed(e);
377 hydrophobicityColour.setText("By hydrophobicity");
378 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
380 public void actionPerformed(ActionEvent e)
382 hydrophobicityColour_actionPerformed(e);
385 helixColour.setText("Helix propensity");
386 helixColour.addActionListener(new java.awt.event.ActionListener()
388 public void actionPerformed(ActionEvent e)
390 helixColour_actionPerformed(e);
393 strandColour.setText("Strand propensity");
394 strandColour.addActionListener(new java.awt.event.ActionListener()
396 public void actionPerformed(ActionEvent e)
398 strandColour_actionPerformed(e);
401 turnColour.setText("Turn propensity");
402 turnColour.addActionListener(new java.awt.event.ActionListener()
404 public void actionPerformed(ActionEvent e)
406 turnColour_actionPerformed(e);
409 buriedColour.setText("Buried index");
410 buriedColour.addActionListener(new java.awt.event.ActionListener()
412 public void actionPerformed(ActionEvent e)
414 buriedColour_actionPerformed(e);
417 userDefinedColour.setText("User defined colours");
418 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
420 public void actionPerformed(ActionEvent e)
422 userDefinedColour_actionPerformed(e);
425 PIDColour.setText("Percentage Identity");
426 PIDColour.addActionListener(new java.awt.event.ActionListener()
428 public void actionPerformed(ActionEvent e)
430 PIDColour_actionPerformed(e);
433 BLOSUM62Colour.setText("BLOSUM62 score");
434 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
436 public void actionPerformed(ActionEvent e)
438 BLOSUM62Colour_actionPerformed(e);
441 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
442 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
444 public void actionPerformed(ActionEvent e)
446 avTreeBlosumMenuItem_actionPerformed(e);
449 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
450 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
452 public void actionPerformed(ActionEvent e)
454 njTreeBlosumMenuItem_actionPerformed(e);
457 annotationPanelMenuItem.setActionCommand("");
458 annotationPanelMenuItem.setText("Annotation Panel");
459 annotationPanelMenuItem.setState(true);
460 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
462 public void actionPerformed(ActionEvent e)
464 annotationPanelMenuItem_actionPerformed(e);
467 colourTextMenuItem.setText("Colour text");
468 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
470 public void actionPerformed(ActionEvent e)
472 colourTextMenuItem_actionPerformed(e);
475 htmlMenuItem.setText("Output as HTML");
476 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
478 public void actionPerformed(ActionEvent e)
480 htmlMenuItem_actionPerformed(e);
483 overviewMenuItem.setText("Overview window");
484 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
486 public void actionPerformed(ActionEvent e)
488 overviewMenuItem_actionPerformed(e);
491 undoMenuItem.setEnabled(false);
492 undoMenuItem.setMnemonic('Z');
493 undoMenuItem.setText("Undo");
494 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
496 public void actionPerformed(ActionEvent e)
498 undoMenuItem_actionPerformed(e);
501 redoMenuItem.setEnabled(false);
502 redoMenuItem.setMnemonic('0');
503 redoMenuItem.setText("Redo");
504 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
506 public void actionPerformed(ActionEvent e)
508 redoMenuItem_actionPerformed(e);
511 conservationMenuItem.setText("By conservation");
512 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
514 public void actionPerformed(ActionEvent e)
516 conservationMenuItem_actionPerformed(e);
519 noColourmenuItem.setText("None");
520 noColourmenuItem.setSelected(true);
521 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
523 public void actionPerformed(ActionEvent e)
525 noColourmenuItem_actionPerformed(e);
528 wrapMenuItem.setText("Wrap alignment");
529 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
531 public void actionPerformed(ActionEvent e)
533 wrapMenuItem_actionPerformed(e);
536 printMenuItem.setText("Print");
537 printMenuItem.addActionListener(new java.awt.event.ActionListener()
539 public void actionPerformed(ActionEvent e)
541 printMenuItem_actionPerformed(e);
544 renderGapsMenuItem.setText("Render gaps");
545 renderGapsMenuItem.setState(true);
546 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
548 public void actionPerformed(ActionEvent e)
550 renderGapsMenuItem_actionPerformed(e);
553 findMenuItem.setText("Find");
554 findMenuItem.addActionListener(new java.awt.event.ActionListener()
556 public void actionPerformed(ActionEvent e)
558 findMenuItem_actionPerformed(e);
561 searchMenu.setText("Search");
563 abovePIDThreshold.setText("Above PID threshold");
564 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
565 public void actionPerformed(ActionEvent e) {
566 abovePIDThreshold_actionPerformed(e);
569 sequenceFeatures.setText("Sequence Features");
570 sequenceFeatures.addActionListener(new ActionListener()
572 public void actionPerformed(ActionEvent actionEvent)
574 sequenceFeatures_actionPerformed(actionEvent);
577 nucleotideColour.setText("Nucleotide colours");
578 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
580 public void actionPerformed(ActionEvent e)
582 nucleotideColour_actionPerformed(e);
585 deleteGroups.setSelected(false);
586 deleteGroups.setText("Delete all groups");
587 deleteGroups.addActionListener(new java.awt.event.ActionListener()
589 public void actionPerformed(ActionEvent e)
591 deleteGroups_actionPerformed(e);
594 copy.setText("Copy");
595 copy.setMnemonic(KeyEvent.VK_C);
597 copy.addActionListener(new java.awt.event.ActionListener()
599 public void actionPerformed(ActionEvent e)
601 copy_actionPerformed(e);
605 cut.setMnemonic(KeyEvent.VK_X);
606 cut.addActionListener(new java.awt.event.ActionListener()
608 public void actionPerformed(ActionEvent e)
610 cut_actionPerformed(e);
613 delete.setText("Delete");
614 delete.addActionListener(new java.awt.event.ActionListener()
616 public void actionPerformed(ActionEvent e)
618 delete_actionPerformed(e);
621 jMenu1.setMnemonic('V');
622 jMenu1.setText("Paste");
623 pasteNew.setText("to new alignment");
624 pasteNew.addActionListener(new java.awt.event.ActionListener()
626 public void actionPerformed(ActionEvent e)
628 pasteNew_actionPerformed(e);
631 pasteThis.setText("add to this alignment");
632 pasteThis.addActionListener(new java.awt.event.ActionListener()
634 public void actionPerformed(ActionEvent e)
636 pasteThis_actionPerformed(e);
639 applyToAllGroups.setText("Apply colour to all groups");
640 applyToAllGroups.setState(true);
641 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
643 public void actionPerformed(ActionEvent e)
645 applyToAllGroups_actionPerformed(e);
648 createPNG.addActionListener(new java.awt.event.ActionListener()
650 public void actionPerformed(ActionEvent e)
652 createPNG_actionPerformed(e);
655 createPNG.setActionCommand("Save as PNG Image");
656 createPNG.setText("Save as PNG Image");
657 font.setText("Change Font");
658 font.addActionListener(new java.awt.event.ActionListener()
660 public void actionPerformed(ActionEvent e)
662 font_actionPerformed(e);
665 fullSeqId.setText("Show full sequence id");
666 fullSeqId.addActionListener(new java.awt.event.ActionListener()
668 public void actionPerformed(ActionEvent e)
670 fullSeqId_actionPerformed(e);
673 epsFile.setText("Save as EPS file");
674 epsFile.addActionListener(new java.awt.event.ActionListener()
676 public void actionPerformed(ActionEvent e)
678 epsFile_actionPerformed(e);
681 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
682 LoadtreeMenuItem.setText("Load assocated tree");
683 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
684 public void actionPerformed(ActionEvent e)
686 LoadtreeMenuItem_actionPerformed(e);
689 jpred.setText("JPred");
690 jpred.addActionListener(new java.awt.event.ActionListener()
692 public void actionPerformed(ActionEvent e)
694 jpred_actionPerformed(e);
697 scaleAbove.setVisible(false);
698 scaleAbove.setText("Scale above alignment");
699 scaleAbove.addActionListener(new java.awt.event.ActionListener()
701 public void actionPerformed(ActionEvent e)
703 scaleAbove_actionPerformed(e);
706 scaleLeft.setVisible(false);
707 scaleLeft.setSelected(true);
708 scaleLeft.setText("Scale left of sequence");
709 scaleLeft.addActionListener(new java.awt.event.ActionListener()
711 public void actionPerformed(ActionEvent e)
713 scaleLeft_actionPerformed(e);
716 scaleRight.setVisible(false);
717 scaleRight.setSelected(true);
718 scaleRight.setText("Scale right of sequence");
719 scaleRight.addActionListener(new java.awt.event.ActionListener()
721 public void actionPerformed(ActionEvent e)
723 scaleRight_actionPerformed(e);
726 modifyPID.setText("Modify PID Threshold");
727 modifyPID.addActionListener(new java.awt.event.ActionListener()
729 public void actionPerformed(ActionEvent e)
731 modifyPID_actionPerformed(e);
734 modifyConservation.setText("Modify Conservation Threshold");
735 modifyConservation.addActionListener(new java.awt.event.ActionListener()
737 public void actionPerformed(ActionEvent e)
739 modifyConservation_actionPerformed(e);
742 sortByTreeMenu.setText("Sort by tree order");
743 alignFrameMenuBar.add(fileMenu);
744 alignFrameMenuBar.add(editMenu);
745 alignFrameMenuBar.add(searchMenu);
746 alignFrameMenuBar.add(viewMenu);
747 alignFrameMenuBar.add(colourMenu);
748 alignFrameMenuBar.add(calculateMenu);
749 alignFrameMenuBar.add(alignMenu);
750 fileMenu.add(saveAlignmentMenu);
751 fileMenu.add(outputTextboxMenu);
752 fileMenu.add(htmlMenuItem);
753 fileMenu.add(epsFile);
754 fileMenu.add(createPNG);
755 fileMenu.add(printMenuItem);
756 fileMenu.addSeparator();
757 fileMenu.add(LoadtreeMenuItem);
758 fileMenu.addSeparator();
759 fileMenu.add(closeMenuItem);
761 editMenu.add(jMenu1);
763 editMenu.add(delete);
764 editMenu.addSeparator();
765 editMenu.add(undoMenuItem);
766 editMenu.add(redoMenuItem);
767 editMenu.addSeparator();
768 editMenu.add(deselectAllSequenceMenuItem);
769 editMenu.add(selectAllSequenceMenuItem);
770 editMenu.add(invertSequenceMenuItem);
771 editMenu.add(deleteGroups);
772 editMenu.addSeparator();
773 editMenu.add(deselectAllColumnsMenuItem);
774 editMenu.add(remove2LeftMenuItem);
775 editMenu.add(remove2RightMenuItem);
776 editMenu.addSeparator();
777 editMenu.add(removeGappedColumnMenuItem);
778 editMenu.add(removeAllGapsMenuItem);
779 editMenu.add(setGapCharMenuItem);
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(overviewMenuItem);
795 viewMenu.add(sequenceFeatures);
796 colourMenu.add(applyToAllGroups);
797 colourMenu.add(noColourmenuItem);
798 colourMenu.add(clustalColour);
799 colourMenu.add(zappoColour);
800 colourMenu.add(taylorColour);
801 colourMenu.add(hydrophobicityColour);
802 colourMenu.add(helixColour);
803 colourMenu.add(strandColour);
804 colourMenu.add(turnColour);
805 colourMenu.add(buriedColour);
806 colourMenu.add(nucleotideColour);
807 colourMenu.add(userDefinedColour);
808 colourMenu.add(PIDColour);
809 colourMenu.add(BLOSUM62Colour);
810 colourMenu.addSeparator();
811 colourMenu.add(conservationMenuItem);
812 colourMenu.add(modifyConservation);
813 colourMenu.add(abovePIDThreshold);
814 colourMenu.add(modifyPID);
815 calculateMenu.add(sortPairwiseMenuItem);
816 calculateMenu.add(sortIDMenuItem);
817 calculateMenu.add(sortGroupMenuItem);
818 calculateMenu.add(sortByTreeMenu);
819 calculateMenu.add(removeRedundancyMenuItem);
820 calculateMenu.addSeparator();
821 calculateMenu.add(pairwiseAlignmentMenuItem);
822 calculateMenu.add(PCAMenuItem);
823 calculateMenu.addSeparator();
824 calculateMenu.add(averageDistanceTreeMenuItem);
825 calculateMenu.add(neighbourTreeMenuItem);
826 calculateMenu.add(avDistanceTreeBlosumMenuItem);
827 calculateMenu.add(njTreeBlosumMenuItem);
828 alignMenu.add(clustalAlignMenuItem);
829 alignMenu.add(msaAlignMenuItem);
830 alignMenu.add(jpred);
831 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
832 jMenu1.add(pasteNew);
833 jMenu1.add(pasteThis);
836 protected void saveAs_actionPerformed(ActionEvent e)
841 protected void outputText_actionPerformed(ActionEvent e)
846 protected void htmlMenuItem_actionPerformed(ActionEvent e)
855 protected void closeMenuItem_actionPerformed(ActionEvent e)
860 protected void redoMenuItem_actionPerformed(ActionEvent e)
865 protected void undoMenuItem_actionPerformed(ActionEvent e)
873 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
878 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
883 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
889 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
894 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
899 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
904 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
909 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
914 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
923 protected void wrapMenuItem_actionPerformed(ActionEvent e)
929 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
934 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
940 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
947 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
952 protected void overviewMenuItem_actionPerformed(ActionEvent e)
957 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
962 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
967 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
973 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
978 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
983 protected void PCAMenuItem_actionPerformed(ActionEvent e)
988 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
993 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
999 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1004 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1011 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
1016 protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
1022 protected void clustalColour_actionPerformed(ActionEvent e)
1027 protected void zappoColour_actionPerformed(ActionEvent e)
1032 protected void taylorColour_actionPerformed(ActionEvent e)
1038 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1043 protected void helixColour_actionPerformed(ActionEvent e)
1048 protected void strandColour_actionPerformed(ActionEvent e)
1053 protected void turnColour_actionPerformed(ActionEvent e)
1058 protected void buriedColour_actionPerformed(ActionEvent e)
1065 protected void userDefinedColour_actionPerformed(ActionEvent e)
1070 protected void PIDColour_actionPerformed(ActionEvent e)
1075 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1081 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1086 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1092 protected void printMenuItem_actionPerformed(ActionEvent e)
1097 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1102 protected void findMenuItem_actionPerformed(ActionEvent e)
1108 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
1112 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
1117 protected void nucleotideColour_actionPerformed(ActionEvent e)
1122 protected void deleteGroups_actionPerformed(ActionEvent e)
1127 protected void copy_actionPerformed(ActionEvent e)
1133 protected void cut_actionPerformed(ActionEvent e)
1138 protected void delete_actionPerformed(ActionEvent e)
1143 protected void pasteNew_actionPerformed(ActionEvent e)
1148 protected void pasteThis_actionPerformed(ActionEvent e)
1153 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1158 protected void createPNG_actionPerformed(ActionEvent e)
1163 protected void font_actionPerformed(ActionEvent e)
1168 protected void fullSeqId_actionPerformed(ActionEvent e)
1173 protected void epsFile_actionPerformed(ActionEvent e)
1178 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1182 protected void jpred_actionPerformed(ActionEvent e)
1187 protected void scaleAbove_actionPerformed(ActionEvent e)
1192 protected void scaleLeft_actionPerformed(ActionEvent e)
1197 protected void scaleRight_actionPerformed(ActionEvent e)
1202 protected void modifyPID_actionPerformed(ActionEvent e)
1207 protected void modifyConservation_actionPerformed(ActionEvent e)