2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.jbgui;
22 import java.awt.event.*;
25 import javax.swing.event.*;
27 import jalview.schemes.*;
29 public class GAlignFrame
30 extends JInternalFrame
32 protected JMenuBar alignFrameMenuBar = new JMenuBar();
33 protected JMenu fileMenu = new JMenu();
34 protected JMenuItem closeMenuItem = new JMenuItem();
35 protected JMenu editMenu = new JMenu();
36 protected JMenu viewMenu = new JMenu();
37 protected JMenu colourMenu = new JMenu();
38 protected JMenu calculateMenu = new JMenu();
39 protected JMenu webService = new JMenu();
40 protected JMenuItem webServiceNoServices;
41 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
42 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
43 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
44 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
45 protected JMenuItem remove2RightMenuItem = new JMenuItem();
46 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
47 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
48 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
49 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
50 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
51 protected JMenuItem sortIDMenuItem = new JMenuItem();
52 protected JMenuItem sortGroupMenuItem = new JMenuItem();
53 protected JMenu sortByAnnotScore = new JMenu();
54 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
55 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
56 protected JMenuItem PCAMenuItem = new JMenuItem();
57 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
58 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
59 BorderLayout borderLayout1 = new BorderLayout();
60 public JLabel statusBar = new JLabel();
61 protected JMenuItem saveAs = new JMenuItem();
62 protected JMenu outputTextboxMenu = new JMenu();
63 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
64 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
65 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
66 protected JRadioButtonMenuItem hydrophobicityColour = new
67 JRadioButtonMenuItem();
68 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
69 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
70 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
71 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
72 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
73 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
74 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
75 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
76 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
77 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
78 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
79 JMenuItem htmlMenuItem = new JMenuItem();
80 JMenuItem overviewMenuItem = new JMenuItem();
81 protected JMenuItem undoMenuItem = new JMenuItem();
82 protected JMenuItem redoMenuItem = new JMenuItem();
83 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
84 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
85 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
86 JMenuItem printMenuItem = new JMenuItem();
87 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
88 JMenuItem findMenuItem = new JMenuItem();
89 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
90 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
91 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
92 JMenuItem deleteGroups = new JMenuItem();
93 JMenuItem delete = new JMenuItem();
94 JMenuItem copy = new JMenuItem();
95 JMenuItem cut = new JMenuItem();
96 JMenu pasteMenu = new JMenu();
97 JMenuItem pasteNew = new JMenuItem();
98 JMenuItem pasteThis = new JMenuItem();
99 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
100 JMenuItem createPNG = new JMenuItem();
101 protected JMenuItem font = new JMenuItem();
102 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
103 JMenuItem epsFile = new JMenuItem();
104 JMenuItem LoadtreeMenuItem = new JMenuItem();
105 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
106 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
107 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
108 protected JMenuItem modifyPID = new JMenuItem();
109 protected JMenuItem modifyConservation = new JMenuItem();
110 protected JMenu sortByTreeMenu = new JMenu();
111 protected JMenu sort = new JMenu();
112 JMenu calculate = new JMenu();
113 JMenu jMenu2 = new JMenu();
114 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
115 protected ButtonGroup colours = new ButtonGroup();
116 JMenuItem vamsasStore = new JMenuItem();
117 protected JMenuItem showTranslation = new JMenuItem();
118 protected JMenuItem extractScores = new JMenuItem();
119 protected JMenu showProducts = new JMenu();
120 public JMenuItem featureSettings = new JMenuItem();
121 JMenuItem fetchSequence = new JMenuItem();
122 JMenuItem annotationColour = new JMenuItem();
123 JMenuItem associatedData = new JMenuItem();
124 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
125 JMenu addSequenceMenu = new JMenu();
126 JMenuItem addFromFile = new JMenuItem();
127 JMenuItem addFromText = new JMenuItem();
128 JMenuItem addFromURL = new JMenuItem();
129 JMenuItem exportAnnotations = new JMenuItem();
130 JMenuItem exportFeatures = new JMenuItem();
131 protected JPanel statusPanel = new JPanel();
132 GridLayout gridLayout1 = new GridLayout();
133 JMenu jMenu3 = new JMenu();
134 JMenuItem showAllSeqs = new JMenuItem();
135 JMenuItem showAllColumns = new JMenuItem();
136 JMenu hideMenu = new JMenu();
137 JMenuItem hideSelSequences = new JMenuItem();
138 JMenuItem hideSelColumns = new JMenuItem();
139 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
140 JMenuItem invertColSel = new JMenuItem();
141 protected JTabbedPane tabbedPane = new JTabbedPane();
142 JMenuItem save = new JMenuItem();
143 protected JMenuItem reload = new JMenuItem();
144 JMenuItem newView = new JMenuItem();
145 JMenuItem textColour = new JMenuItem();
146 JMenu formatMenu = new JMenu();
147 JMenu selectMenu = new JMenu();
148 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
149 protected JMenuItem gatherViews = new JMenuItem();
150 protected JMenuItem expandViews = new JMenuItem();
151 JMenuItem pageSetup = new JMenuItem();
152 JMenuItem alignmentProperties = new JMenuItem();
158 setJMenuBar(alignFrameMenuBar);
160 // dynamically fill save as menu with available formats
161 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
163 JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.
164 WRITEABLE_FORMATS[i]);
166 item.addActionListener(new java.awt.event.ActionListener()
168 public void actionPerformed(ActionEvent e)
170 outputText_actionPerformed(e);
174 outputTextboxMenu.add(item);
181 if (!new jalview.util.Platform().isAMac())
183 closeMenuItem.setMnemonic('C');
184 outputTextboxMenu.setMnemonic('T');
185 undoMenuItem.setMnemonic('Z');
186 redoMenuItem.setMnemonic('0');
187 copy.setMnemonic('C');
188 cut.setMnemonic('U');
189 pasteMenu.setMnemonic('P');
190 reload.setMnemonic('R');
193 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
195 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
196 getUserColourSchemes().keys();
198 while (userColours.hasMoreElements())
200 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
202 nextElement().toString());
203 radioItem.setName("USER_DEFINED");
204 radioItem.addMouseListener(new MouseAdapter()
206 public void mousePressed(MouseEvent evt)
208 if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
210 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
212 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
214 "Remove from default list?",
215 "Remove user defined colour",
216 JOptionPane.YES_NO_OPTION);
217 if (option == JOptionPane.YES_OPTION)
219 jalview.gui.UserDefinedColours.removeColourFromDefaults(
220 radioItem.getText());
221 colourMenu.remove(radioItem);
225 radioItem.addActionListener(new ActionListener()
227 public void actionPerformed(ActionEvent evt)
229 userDefinedColour_actionPerformed(evt);
236 radioItem.addActionListener(new ActionListener()
238 public void actionPerformed(ActionEvent evt)
240 userDefinedColour_actionPerformed(evt);
243 colourMenu.insert(radioItem, 15);
244 colours.add(radioItem);
247 colours.add(noColourmenuItem);
248 colours.add(clustalColour);
249 colours.add(zappoColour);
250 colours.add(taylorColour);
251 colours.add(hydrophobicityColour);
252 colours.add(helixColour);
253 colours.add(strandColour);
254 colours.add(turnColour);
255 colours.add(buriedColour);
256 colours.add(userDefinedColour);
257 colours.add(PIDColour);
258 colours.add(BLOSUM62Colour);
259 colours.add(nucleotideColour);
261 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
265 public void setColourSelected(String defaultColour)
268 if (defaultColour != null)
270 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
274 case ColourSchemeProperty.NONE:
275 noColourmenuItem.setSelected(true);
277 case ColourSchemeProperty.CLUSTAL:
278 clustalColour.setSelected(true);
282 case ColourSchemeProperty.BLOSUM:
283 BLOSUM62Colour.setSelected(true);
287 case ColourSchemeProperty.PID:
288 PIDColour.setSelected(true);
292 case ColourSchemeProperty.ZAPPO:
293 zappoColour.setSelected(true);
297 case ColourSchemeProperty.TAYLOR:
298 taylorColour.setSelected(true);
301 case ColourSchemeProperty.HYDROPHOBIC:
302 hydrophobicityColour.setSelected(true);
306 case ColourSchemeProperty.HELIX:
307 helixColour.setSelected(true);
311 case ColourSchemeProperty.STRAND:
312 strandColour.setSelected(true);
316 case ColourSchemeProperty.TURN:
317 turnColour.setSelected(true);
321 case ColourSchemeProperty.BURIED:
322 buriedColour.setSelected(true);
326 case ColourSchemeProperty.NUCLEOTIDE:
327 nucleotideColour.setSelected(true);
331 case ColourSchemeProperty.USER_DEFINED:
332 userDefinedColour.setSelected(true);
340 private void jbInit()
343 fileMenu.setText("File");
344 saveAs.setText("Save As...");
345 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
347 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
348 java.awt.event.KeyEvent.SHIFT_MASK, false));
349 saveAs.addActionListener(new ActionListener()
351 public void actionPerformed(ActionEvent e)
353 saveAs_actionPerformed(e);
356 closeMenuItem.setText("Close");
357 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
358 event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
359 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
361 public void actionPerformed(ActionEvent e)
363 closeMenuItem_actionPerformed(false);
366 editMenu.setText("Edit");
367 viewMenu.setText("View");
368 colourMenu.setText("Colour");
369 calculateMenu.setText("Calculate");
370 webService.setText("Web Service");
371 selectAllSequenceMenuItem.setText("Select All");
372 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
373 java.awt.event.KeyEvent.VK_A,
374 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
375 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
378 public void actionPerformed(ActionEvent e)
380 selectAllSequenceMenuItem_actionPerformed(e);
383 deselectAllSequenceMenuItem.setText("Deselect All");
384 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
386 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
387 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
390 public void actionPerformed(ActionEvent e)
392 deselectAllSequenceMenuItem_actionPerformed(e);
395 invertSequenceMenuItem.setText("Invert Sequence Selection");
396 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
397 java.awt.event.KeyEvent.VK_I,
398 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
399 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
401 public void actionPerformed(ActionEvent e)
403 invertSequenceMenuItem_actionPerformed(e);
406 remove2LeftMenuItem.setText("Remove Left");
407 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
408 awt.event.KeyEvent.VK_L,
409 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
410 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
412 public void actionPerformed(ActionEvent e)
414 remove2LeftMenuItem_actionPerformed(e);
417 remove2RightMenuItem.setText("Remove Right");
418 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
419 awt.event.KeyEvent.VK_R,
420 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
421 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
423 public void actionPerformed(ActionEvent e)
425 remove2RightMenuItem_actionPerformed(e);
428 removeGappedColumnMenuItem.setText("Remove Empty Columns");
429 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
430 getKeyStroke(java.awt.event.
431 KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
432 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
435 public void actionPerformed(ActionEvent e)
437 removeGappedColumnMenuItem_actionPerformed(e);
440 removeAllGapsMenuItem.setText("Remove All Gaps");
441 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
442 java.awt.event.KeyEvent.VK_E,
443 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
444 java.awt.event.KeyEvent.SHIFT_MASK, false));
445 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
447 public void actionPerformed(ActionEvent e)
449 removeAllGapsMenuItem_actionPerformed(e);
452 viewBoxesMenuItem.setText("Boxes");
453 viewBoxesMenuItem.setState(true);
454 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
456 public void actionPerformed(ActionEvent e)
458 viewBoxesMenuItem_actionPerformed(e);
461 viewTextMenuItem.setText("Text");
462 viewTextMenuItem.setState(true);
463 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
465 public void actionPerformed(ActionEvent e)
467 viewTextMenuItem_actionPerformed(e);
470 sortPairwiseMenuItem.setText("by Pairwise Identity");
471 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
473 public void actionPerformed(ActionEvent e)
475 sortPairwiseMenuItem_actionPerformed(e);
478 sortIDMenuItem.setText("by ID");
479 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
481 public void actionPerformed(ActionEvent e)
483 sortIDMenuItem_actionPerformed(e);
486 sortGroupMenuItem.setText("by Group");
487 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
489 public void actionPerformed(ActionEvent e)
491 sortGroupMenuItem_actionPerformed(e);
494 removeRedundancyMenuItem.setText("Remove Redundancy...");
495 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
496 java.awt.event.KeyEvent.VK_D,
497 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
498 removeRedundancyMenuItem.addActionListener(new java.awt.event.
501 public void actionPerformed(ActionEvent e)
503 removeRedundancyMenuItem_actionPerformed(e);
506 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
507 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
510 public void actionPerformed(ActionEvent e)
512 pairwiseAlignmentMenuItem_actionPerformed(e);
515 PCAMenuItem.setText("Principal Component Analysis");
516 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
518 public void actionPerformed(ActionEvent e)
520 PCAMenuItem_actionPerformed(e);
523 averageDistanceTreeMenuItem.setText(
524 "Average Distance Using % Identity");
525 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
528 public void actionPerformed(ActionEvent e)
530 averageDistanceTreeMenuItem_actionPerformed(e);
533 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
534 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
536 public void actionPerformed(ActionEvent e)
538 neighbourTreeMenuItem_actionPerformed(e);
541 this.getContentPane().setLayout(borderLayout1);
542 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
543 statusBar.setBackground(Color.white);
544 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
545 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
546 statusBar.setText("Status bar");
547 outputTextboxMenu.setText("Output to Textbox");
548 clustalColour.setText("Clustalx");
550 clustalColour.addActionListener(new java.awt.event.ActionListener()
552 public void actionPerformed(ActionEvent e)
554 clustalColour_actionPerformed(e);
557 zappoColour.setText("Zappo");
558 zappoColour.addActionListener(new java.awt.event.ActionListener()
560 public void actionPerformed(ActionEvent e)
562 zappoColour_actionPerformed(e);
565 taylorColour.setText("Taylor");
566 taylorColour.addActionListener(new java.awt.event.ActionListener()
568 public void actionPerformed(ActionEvent e)
570 taylorColour_actionPerformed(e);
573 hydrophobicityColour.setText("Hydrophobicity");
574 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
576 public void actionPerformed(ActionEvent e)
578 hydrophobicityColour_actionPerformed(e);
581 helixColour.setText("Helix Propensity");
582 helixColour.addActionListener(new java.awt.event.ActionListener()
584 public void actionPerformed(ActionEvent e)
586 helixColour_actionPerformed(e);
589 strandColour.setText("Strand Propensity");
590 strandColour.addActionListener(new java.awt.event.ActionListener()
592 public void actionPerformed(ActionEvent e)
594 strandColour_actionPerformed(e);
597 turnColour.setText("Turn Propensity");
598 turnColour.addActionListener(new java.awt.event.ActionListener()
600 public void actionPerformed(ActionEvent e)
602 turnColour_actionPerformed(e);
605 buriedColour.setText("Buried Index");
606 buriedColour.addActionListener(new java.awt.event.ActionListener()
608 public void actionPerformed(ActionEvent e)
610 buriedColour_actionPerformed(e);
613 userDefinedColour.setText("User Defined...");
614 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
616 public void actionPerformed(ActionEvent e)
618 userDefinedColour_actionPerformed(e);
621 PIDColour.setText("Percentage Identity");
622 PIDColour.addActionListener(new java.awt.event.ActionListener()
624 public void actionPerformed(ActionEvent e)
626 PIDColour_actionPerformed(e);
629 BLOSUM62Colour.setText("BLOSUM62 Score");
630 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
632 public void actionPerformed(ActionEvent e)
634 BLOSUM62Colour_actionPerformed(e);
637 avDistanceTreeBlosumMenuItem.setText(
638 "Average Distance Using BLOSUM62");
639 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
642 public void actionPerformed(ActionEvent e)
644 avTreeBlosumMenuItem_actionPerformed(e);
647 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
648 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
650 public void actionPerformed(ActionEvent e)
652 njTreeBlosumMenuItem_actionPerformed(e);
655 annotationPanelMenuItem.setActionCommand("");
656 annotationPanelMenuItem.setText("Show Annotations");
657 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
658 "SHOW_ANNOTATIONS", true));
659 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
661 public void actionPerformed(ActionEvent e)
663 annotationPanelMenuItem_actionPerformed(e);
666 colourTextMenuItem.setText("Colour Text");
667 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
669 public void actionPerformed(ActionEvent e)
671 colourTextMenuItem_actionPerformed(e);
674 htmlMenuItem.setText("HTML");
675 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
677 public void actionPerformed(ActionEvent e)
679 htmlMenuItem_actionPerformed(e);
682 overviewMenuItem.setText("Overview Window");
683 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
685 public void actionPerformed(ActionEvent e)
687 overviewMenuItem_actionPerformed(e);
690 undoMenuItem.setEnabled(false);
691 undoMenuItem.setText("Undo");
692 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
693 java.awt.event.KeyEvent.VK_Z,
694 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
695 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
697 public void actionPerformed(ActionEvent e)
699 undoMenuItem_actionPerformed(e);
702 redoMenuItem.setEnabled(false);
703 redoMenuItem.setText("Redo");
704 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
705 event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
706 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
708 public void actionPerformed(ActionEvent e)
710 redoMenuItem_actionPerformed(e);
713 conservationMenuItem.setText("By Conservation");
714 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
716 public void actionPerformed(ActionEvent e)
718 conservationMenuItem_actionPerformed(e);
721 noColourmenuItem.setText("None");
722 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
724 public void actionPerformed(ActionEvent e)
726 noColourmenuItem_actionPerformed(e);
729 wrapMenuItem.setText("Wrap");
730 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
732 public void actionPerformed(ActionEvent e)
734 wrapMenuItem_actionPerformed(e);
737 printMenuItem.setText("Print ...");
738 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
739 event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
740 printMenuItem.addActionListener(new java.awt.event.ActionListener()
742 public void actionPerformed(ActionEvent e)
744 printMenuItem_actionPerformed(e);
747 renderGapsMenuItem.setText("Show Gaps");
748 renderGapsMenuItem.setState(true);
749 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
751 public void actionPerformed(ActionEvent e)
753 renderGapsMenuItem_actionPerformed(e);
756 findMenuItem.setText("Find...");
757 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
758 java.awt.event.KeyEvent.VK_F,
759 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
760 findMenuItem.addActionListener(new java.awt.event.ActionListener()
762 public void actionPerformed(ActionEvent e)
764 findMenuItem_actionPerformed(e);
767 abovePIDThreshold.setText("Above Identity Threshold");
768 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
770 public void actionPerformed(ActionEvent e)
772 abovePIDThreshold_actionPerformed(e);
775 showSeqFeatures.setText("Show Sequence Features");
776 showSeqFeatures.addActionListener(new ActionListener()
778 public void actionPerformed(ActionEvent actionEvent)
780 showSeqFeatures_actionPerformed(actionEvent);
783 nucleotideColour.setText("Nucleotide");
784 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
786 public void actionPerformed(ActionEvent e)
788 nucleotideColour_actionPerformed(e);
791 deleteGroups.setText("Undefine groups");
792 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
793 event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
794 deleteGroups.addActionListener(new java.awt.event.ActionListener()
796 public void actionPerformed(ActionEvent e)
798 deleteGroups_actionPerformed(e);
801 copy.setText("Copy");
802 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
803 java.awt.event.KeyEvent.VK_C,
804 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
806 copy.addActionListener(new java.awt.event.ActionListener()
808 public void actionPerformed(ActionEvent e)
810 copy_actionPerformed(e);
814 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
815 java.awt.event.KeyEvent.VK_X,
816 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
817 cut.addActionListener(new java.awt.event.ActionListener()
819 public void actionPerformed(ActionEvent e)
821 cut_actionPerformed(e);
824 delete.setText("Delete");
825 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
826 KeyEvent.VK_BACK_SPACE, 0, false));
827 delete.addActionListener(new java.awt.event.ActionListener()
829 public void actionPerformed(ActionEvent e)
831 delete_actionPerformed(e);
834 pasteMenu.setText("Paste");
835 pasteNew.setText("To New Alignment");
836 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
837 java.awt.event.KeyEvent.VK_V,
838 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
839 java.awt.event.KeyEvent.SHIFT_MASK, false));
840 pasteNew.addActionListener(new java.awt.event.ActionListener()
842 public void actionPerformed(ActionEvent e)
844 pasteNew_actionPerformed(e);
847 pasteThis.setText("Add To This Alignment");
848 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
849 java.awt.event.KeyEvent.VK_V,
850 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
851 pasteThis.addActionListener(new java.awt.event.ActionListener()
853 public void actionPerformed(ActionEvent e)
855 pasteThis_actionPerformed(e);
858 applyToAllGroups.setText("Apply Colour To All Groups");
859 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
861 public void actionPerformed(ActionEvent e)
863 applyToAllGroups_actionPerformed(e);
866 createPNG.addActionListener(new java.awt.event.ActionListener()
868 public void actionPerformed(ActionEvent e)
873 createPNG.setActionCommand("Save As PNG Image");
874 createPNG.setText("PNG");
875 font.setText("Font...");
876 font.addActionListener(new java.awt.event.ActionListener()
878 public void actionPerformed(ActionEvent e)
880 font_actionPerformed(e);
884 seqLimits.setText("Show Sequence Limits");
885 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
886 seqLimits.addActionListener(new java.awt.event.ActionListener()
888 public void actionPerformed(ActionEvent e)
890 seqLimit_actionPerformed(e);
893 epsFile.setText("EPS");
894 epsFile.addActionListener(new java.awt.event.ActionListener()
896 public void actionPerformed(ActionEvent e)
901 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
902 LoadtreeMenuItem.setText("Load Associated Tree");
903 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
905 public void actionPerformed(ActionEvent e)
907 LoadtreeMenuItem_actionPerformed(e);
910 scaleAbove.setVisible(false);
911 scaleAbove.setText("Scale Above");
912 scaleAbove.addActionListener(new java.awt.event.ActionListener()
914 public void actionPerformed(ActionEvent e)
916 scaleAbove_actionPerformed(e);
919 scaleLeft.setVisible(false);
920 scaleLeft.setSelected(true);
921 scaleLeft.setText("Scale Left");
922 scaleLeft.addActionListener(new java.awt.event.ActionListener()
924 public void actionPerformed(ActionEvent e)
926 scaleLeft_actionPerformed(e);
929 scaleRight.setVisible(false);
930 scaleRight.setSelected(true);
931 scaleRight.setText("Scale Right");
932 scaleRight.addActionListener(new java.awt.event.ActionListener()
934 public void actionPerformed(ActionEvent e)
936 scaleRight_actionPerformed(e);
939 modifyPID.setText("Modify Identity Threshold...");
940 modifyPID.addActionListener(new java.awt.event.ActionListener()
942 public void actionPerformed(ActionEvent e)
944 modifyPID_actionPerformed(e);
947 modifyConservation.setText("Modify Conservation Threshold...");
948 modifyConservation.addActionListener(new java.awt.event.ActionListener()
950 public void actionPerformed(ActionEvent e)
952 modifyConservation_actionPerformed(e);
955 sortByTreeMenu.setText("By Tree Order");
956 sort.setText("Sort");
957 sort.addMenuListener(new MenuListener()
959 public void menuSelected(MenuEvent e)
964 public void menuDeselected(MenuEvent e)
968 public void menuCanceled(MenuEvent e)
972 sortByAnnotScore.setText("by Score");
973 sort.add(sortByAnnotScore);
974 sortByAnnotScore.addMenuListener(
975 new javax.swing.event.MenuListener() {
977 public void menuCanceled(MenuEvent e)
981 public void menuDeselected(MenuEvent e)
985 public void menuSelected(MenuEvent e)
987 buildSortByAnnotationScoresMenu();
991 sortByAnnotScore.setVisible(false);
993 calculate.setText("Calculate Tree");
995 jMenu2.setText("Export Image");
996 padGapsMenuitem.setText("Pad Gaps");
997 padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
998 padGapsMenuitem.addActionListener(new ActionListener()
1000 public void actionPerformed(ActionEvent e)
1002 padGapsMenuitem_actionPerformed(e);
1005 vamsasStore.setVisible(false);
1006 vamsasStore.setText("VAMSAS store");
1007 vamsasStore.addActionListener(new ActionListener()
1009 public void actionPerformed(ActionEvent e)
1011 vamsasStore_actionPerformed(e);
1014 showTranslation.setText("Translate cDNA");
1015 showTranslation.addActionListener(new ActionListener()
1017 public void actionPerformed(ActionEvent e)
1019 showTranslation_actionPerformed(e);
1022 extractScores.setText("Extract Scores...");
1023 extractScores.addActionListener(new ActionListener()
1025 public void actionPerformed(ActionEvent e)
1027 extractScores_actionPerformed(e);
1030 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based score extraction
1031 showProducts.setText("Get Cross References");
1032 /*showProducts.addActionListener(new ActionListener()
1035 public void actionPerformed(ActionEvent e)
1037 showProducts_actionPerformed(e);
1040 featureSettings.setText("Feature Settings...");
1041 featureSettings.addActionListener(new ActionListener()
1043 public void actionPerformed(ActionEvent e)
1045 featureSettings_actionPerformed(e);
1048 fetchSequence.setText("Fetch Sequence(s)...");
1049 fetchSequence.addActionListener(new ActionListener()
1051 public void actionPerformed(ActionEvent e)
1053 fetchSequence_actionPerformed(e);
1057 annotationColour.setText("By Annotation...");
1058 annotationColour.addActionListener(new ActionListener()
1060 public void actionPerformed(ActionEvent e)
1062 annotationColour_actionPerformed(e);
1065 associatedData.setText("Load Features / Annotations");
1066 associatedData.addActionListener(new ActionListener()
1068 public void actionPerformed(ActionEvent e)
1070 associatedData_actionPerformed(e);
1073 autoCalculate.setText("Autocalculate Consensus");
1074 autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1075 autoCalculate.addActionListener(new ActionListener()
1077 public void actionPerformed(ActionEvent e)
1079 autoCalculate_actionPerformed(e);
1082 addSequenceMenu.setText("Add Sequences");
1083 addFromFile.setText("From File");
1084 addFromFile.addActionListener(new ActionListener()
1086 public void actionPerformed(ActionEvent e)
1088 addFromFile_actionPerformed(e);
1091 addFromText.setText("From Textbox");
1092 addFromText.addActionListener(new ActionListener()
1094 public void actionPerformed(ActionEvent e)
1096 addFromText_actionPerformed(e);
1099 addFromURL.setText("From URL");
1100 addFromURL.addActionListener(new ActionListener()
1102 public void actionPerformed(ActionEvent e)
1104 addFromURL_actionPerformed(e);
1107 exportFeatures.setText("Export Features...");
1108 exportFeatures.addActionListener(new ActionListener()
1110 public void actionPerformed(ActionEvent e)
1112 exportFeatures_actionPerformed(e);
1115 exportAnnotations.setText("Export Annotations...");
1116 exportAnnotations.addActionListener(new ActionListener()
1118 public void actionPerformed(ActionEvent e)
1120 exportAnnotations_actionPerformed(e);
1123 statusPanel.setLayout(gridLayout1);
1124 jMenu3.setText("Show");
1125 showAllSeqs.setText("All Sequences");
1126 showAllSeqs.addActionListener(new ActionListener()
1128 public void actionPerformed(ActionEvent e)
1130 showAllSeqs_actionPerformed(e);
1133 showAllColumns.setText("All Columns");
1134 showAllColumns.addActionListener(new ActionListener()
1136 public void actionPerformed(ActionEvent e)
1138 showAllColumns_actionPerformed(e);
1141 hideMenu.setText("Hide");
1142 hideSelSequences.setText("Selected Sequences");
1143 hideSelSequences.addActionListener(new ActionListener()
1145 public void actionPerformed(ActionEvent e)
1147 hideSelSequences_actionPerformed(e);
1150 hideSelColumns.setText("Selected Columns");
1151 hideSelColumns.addActionListener(new ActionListener()
1153 public void actionPerformed(ActionEvent e)
1155 hideSelColumns_actionPerformed(e);
1158 hiddenMarkers.setText("Show Hidden Markers");
1159 hiddenMarkers.addActionListener(new ActionListener()
1161 public void actionPerformed(ActionEvent e)
1163 hiddenMarkers_actionPerformed(e);
1166 invertColSel.setText("Invert Column Selection");
1167 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
1168 event.KeyEvent.VK_I,
1169 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1170 | java.awt.event.KeyEvent.ALT_MASK,
1172 invertColSel.addActionListener(new ActionListener()
1174 public void actionPerformed(ActionEvent e)
1176 invertColSel_actionPerformed(e);
1179 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1181 public void stateChanged(ChangeEvent evt)
1183 JTabbedPane pane = (JTabbedPane) evt.getSource();
1184 int sel = pane.getSelectedIndex();
1185 tabSelectionChanged(sel);
1188 tabbedPane.addMouseListener(new MouseAdapter()
1190 public void mousePressed(MouseEvent e)
1192 tabbedPane_mousePressed(e);
1195 tabbedPane.addFocusListener(new FocusAdapter()
1197 public void focusGained(FocusEvent e)
1199 tabbedPane_focusGained(e);
1202 save.setText("Save");
1203 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
1204 KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
1205 save.addActionListener(new ActionListener()
1207 public void actionPerformed(ActionEvent e)
1209 save_actionPerformed(e);
1212 reload.setEnabled(false);
1213 reload.setText("Reload");
1214 reload.addActionListener(new ActionListener()
1216 public void actionPerformed(ActionEvent e)
1218 reload_actionPerformed(e);
1221 newView.setText("New View");
1222 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
1223 KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
1224 newView.addActionListener(new ActionListener()
1226 public void actionPerformed(ActionEvent e)
1228 newView_actionPerformed(e);
1231 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1233 "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1234 textColour.setText("Colour Text ...");
1235 textColour.addActionListener(new ActionListener()
1237 public void actionPerformed(ActionEvent e)
1239 textColour_actionPerformed(e);
1242 formatMenu.setText("Format");
1243 selectMenu.setText("Select");
1244 idRightAlign.setText("Right Align Sequence Id");
1245 idRightAlign.addActionListener(new ActionListener()
1247 public void actionPerformed(ActionEvent e)
1249 idRightAlign_actionPerformed(e);
1252 gatherViews.setEnabled(false);
1253 gatherViews.setText("Gather Views");
1254 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
1255 event.KeyEvent.VK_G, 0, false));
1256 gatherViews.addActionListener(new ActionListener()
1258 public void actionPerformed(ActionEvent e)
1260 gatherViews_actionPerformed(e);
1263 expandViews.setEnabled(false);
1264 expandViews.setText("Expand Views");
1265 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
1266 event.KeyEvent.VK_X, 0, false));
1267 expandViews.addActionListener(new ActionListener()
1269 public void actionPerformed(ActionEvent e)
1271 expandViews_actionPerformed(e);
1274 pageSetup.setText("Page Setup ...");
1275 pageSetup.addActionListener(new ActionListener()
1277 public void actionPerformed(ActionEvent e)
1279 pageSetup_actionPerformed(e);
1282 alignmentProperties.setText("Alignment Properties...");
1283 alignmentProperties.addActionListener(new ActionListener()
1285 public void actionPerformed(ActionEvent actionEvent)
1287 alignmentProperties();
1291 alignFrameMenuBar.add(fileMenu);
1292 alignFrameMenuBar.add(editMenu);
1293 alignFrameMenuBar.add(selectMenu);
1294 alignFrameMenuBar.add(viewMenu);
1295 alignFrameMenuBar.add(formatMenu);
1296 alignFrameMenuBar.add(colourMenu);
1297 alignFrameMenuBar.add(calculateMenu);
1298 alignFrameMenuBar.add(webService);
1299 fileMenu.add(fetchSequence);
1300 fileMenu.add(addSequenceMenu);
1301 fileMenu.add(reload);
1302 fileMenu.addSeparator();
1303 fileMenu.add(vamsasStore);
1305 fileMenu.add(saveAs);
1306 fileMenu.add(outputTextboxMenu);
1307 fileMenu.add(pageSetup);
1308 fileMenu.add(printMenuItem);
1309 fileMenu.addSeparator();
1310 fileMenu.add(jMenu2);
1311 fileMenu.add(exportFeatures);
1312 fileMenu.add(exportAnnotations);
1313 fileMenu.add(LoadtreeMenuItem);
1314 fileMenu.add(associatedData);
1315 fileMenu.addSeparator();
1316 fileMenu.add(closeMenuItem);
1317 editMenu.add(undoMenuItem);
1318 editMenu.add(redoMenuItem);
1321 editMenu.add(pasteMenu);
1322 editMenu.add(delete);
1323 editMenu.addSeparator();
1324 editMenu.add(remove2LeftMenuItem);
1325 editMenu.add(remove2RightMenuItem);
1326 editMenu.add(removeGappedColumnMenuItem);
1327 editMenu.add(removeAllGapsMenuItem);
1328 editMenu.add(removeRedundancyMenuItem);
1329 editMenu.addSeparator();
1330 editMenu.add(padGapsMenuitem);
1331 viewMenu.add(newView);
1332 viewMenu.add(expandViews);
1333 viewMenu.add(gatherViews);
1334 viewMenu.addSeparator();
1335 viewMenu.add(jMenu3);
1336 viewMenu.add(hideMenu);
1337 viewMenu.addSeparator();
1338 viewMenu.add(annotationPanelMenuItem);
1339 viewMenu.addSeparator();
1340 viewMenu.add(showSeqFeatures);
1341 viewMenu.add(featureSettings);
1342 viewMenu.addSeparator();
1343 viewMenu.add(alignmentProperties);
1344 viewMenu.addSeparator();
1345 viewMenu.add(overviewMenuItem);
1346 colourMenu.add(applyToAllGroups);
1347 colourMenu.add(textColour);
1348 colourMenu.addSeparator();
1349 colourMenu.add(noColourmenuItem);
1350 colourMenu.add(clustalColour);
1351 colourMenu.add(BLOSUM62Colour);
1352 colourMenu.add(PIDColour);
1353 colourMenu.add(zappoColour);
1354 colourMenu.add(taylorColour);
1355 colourMenu.add(hydrophobicityColour);
1356 colourMenu.add(helixColour);
1357 colourMenu.add(strandColour);
1358 colourMenu.add(turnColour);
1359 colourMenu.add(buriedColour);
1360 colourMenu.add(nucleotideColour);
1361 colourMenu.add(userDefinedColour);
1362 colourMenu.addSeparator();
1363 colourMenu.add(conservationMenuItem);
1364 colourMenu.add(modifyConservation);
1365 colourMenu.add(abovePIDThreshold);
1366 colourMenu.add(modifyPID);
1367 colourMenu.add(annotationColour);
1368 calculateMenu.add(sort);
1369 calculateMenu.add(calculate);
1370 calculateMenu.addSeparator();
1371 calculateMenu.add(pairwiseAlignmentMenuItem);
1372 calculateMenu.add(PCAMenuItem);
1373 calculateMenu.addSeparator();
1374 calculateMenu.add(showTranslation);
1375 calculateMenu.add(showProducts);
1376 calculateMenu.add(autoCalculate);
1377 calculateMenu.addSeparator();
1378 calculateMenu.add(extractScores);
1379 webServiceNoServices = new JMenuItem("<No Services>");
1380 webService.add(webServiceNoServices);
1381 pasteMenu.add(pasteNew);
1382 pasteMenu.add(pasteThis);
1383 sort.add(sortIDMenuItem);
1384 sort.add(sortGroupMenuItem);
1385 sort.add(sortPairwiseMenuItem);
1386 sort.add(sortByTreeMenu);
1387 calculate.add(averageDistanceTreeMenuItem);
1388 calculate.add(neighbourTreeMenuItem);
1389 calculate.add(avDistanceTreeBlosumMenuItem);
1390 calculate.add(njTreeBlosumMenuItem);
1391 jMenu2.add(htmlMenuItem);
1392 jMenu2.add(epsFile);
1393 jMenu2.add(createPNG);
1394 addSequenceMenu.add(addFromFile);
1395 addSequenceMenu.add(addFromText);
1396 addSequenceMenu.add(addFromURL);
1397 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1398 statusPanel.add(statusBar, null);
1399 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1400 jMenu3.add(showAllColumns);
1401 jMenu3.add(showAllSeqs);
1402 hideMenu.add(hideSelColumns);
1403 hideMenu.add(hideSelSequences);
1404 formatMenu.add(font);
1405 formatMenu.addSeparator();
1406 formatMenu.add(wrapMenuItem);
1407 formatMenu.add(scaleAbove);
1408 formatMenu.add(scaleLeft);
1409 formatMenu.add(scaleRight);
1410 formatMenu.add(seqLimits);
1411 formatMenu.add(idRightAlign);
1412 formatMenu.add(hiddenMarkers);
1413 formatMenu.add(viewBoxesMenuItem);
1414 formatMenu.add(viewTextMenuItem);
1415 formatMenu.add(colourTextMenuItem);
1416 formatMenu.add(renderGapsMenuItem);
1417 selectMenu.add(findMenuItem);
1418 selectMenu.addSeparator();
1419 selectMenu.add(selectAllSequenceMenuItem);
1420 selectMenu.add(deselectAllSequenceMenuItem);
1421 selectMenu.add(invertSequenceMenuItem);
1422 selectMenu.add(invertColSel);
1423 selectMenu.add(deleteGroups);
1426 protected void showProducts_actionPerformed(ActionEvent e)
1428 // TODO Auto-generated method stub
1432 protected void buildSortByAnnotationScoresMenu()
1436 protected void extractScores_actionPerformed(ActionEvent e)
1440 protected void outputText_actionPerformed(ActionEvent e)
1444 public void addFromFile_actionPerformed(ActionEvent e)
1449 public void addFromText_actionPerformed(ActionEvent e)
1454 public void addFromURL_actionPerformed(ActionEvent e)
1459 public void exportFeatures_actionPerformed(ActionEvent e)
1464 public void exportAnnotations_actionPerformed(ActionEvent e)
1469 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1473 protected void closeMenuItem_actionPerformed(boolean b)
1477 protected void redoMenuItem_actionPerformed(ActionEvent e)
1481 protected void undoMenuItem_actionPerformed(ActionEvent e)
1485 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1489 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1493 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1497 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1501 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1505 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1509 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1513 protected void wrapMenuItem_actionPerformed(ActionEvent e)
1517 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1521 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1525 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1529 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1533 protected void overviewMenuItem_actionPerformed(ActionEvent e)
1537 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1541 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1545 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1549 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1553 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1557 protected void PCAMenuItem_actionPerformed(ActionEvent e)
1561 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1565 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1569 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1573 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1577 protected void clustalColour_actionPerformed(ActionEvent e)
1581 protected void zappoColour_actionPerformed(ActionEvent e)
1585 protected void taylorColour_actionPerformed(ActionEvent e)
1589 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1593 protected void helixColour_actionPerformed(ActionEvent e)
1597 protected void strandColour_actionPerformed(ActionEvent e)
1601 protected void turnColour_actionPerformed(ActionEvent e)
1605 protected void buriedColour_actionPerformed(ActionEvent e)
1609 protected void userDefinedColour_actionPerformed(ActionEvent e)
1613 protected void PIDColour_actionPerformed(ActionEvent e)
1617 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1621 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1625 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1629 protected void printMenuItem_actionPerformed(ActionEvent e)
1633 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1637 protected void findMenuItem_actionPerformed(ActionEvent e)
1641 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1645 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
1649 protected void nucleotideColour_actionPerformed(ActionEvent e)
1653 protected void deleteGroups_actionPerformed(ActionEvent e)
1657 protected void copy_actionPerformed(ActionEvent e)
1661 protected void cut_actionPerformed(ActionEvent e)
1665 protected void delete_actionPerformed(ActionEvent e)
1669 protected void pasteNew_actionPerformed(ActionEvent e)
1673 protected void pasteThis_actionPerformed(ActionEvent e)
1677 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1681 public void createPNG(java.io.File f)
1685 protected void font_actionPerformed(ActionEvent e)
1689 protected void seqLimit_actionPerformed(ActionEvent e)
1693 public void seqDBRef_actionPerformed(ActionEvent e)
1698 public void createEPS(java.io.File f)
1702 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
1706 protected void jpred_actionPerformed(ActionEvent e)
1710 protected void scaleAbove_actionPerformed(ActionEvent e)
1714 protected void scaleLeft_actionPerformed(ActionEvent e)
1718 protected void scaleRight_actionPerformed(ActionEvent e)
1722 protected void modifyPID_actionPerformed(ActionEvent e)
1726 protected void modifyConservation_actionPerformed(ActionEvent e)
1730 protected void saveAs_actionPerformed(ActionEvent e)
1734 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
1738 public void vamsasStore_actionPerformed(ActionEvent e)
1743 public void vamsasLoad_actionPerformed(ActionEvent e)
1748 public void showTranslation_actionPerformed(ActionEvent e)
1753 public void featureSettings_actionPerformed(ActionEvent e)
1758 public void fetchSequence_actionPerformed(ActionEvent e)
1763 public void smoothFont_actionPerformed(ActionEvent e)
1768 public void annotationColour_actionPerformed(ActionEvent e)
1773 public void associatedData_actionPerformed(ActionEvent e)
1778 public void autoCalculate_actionPerformed(ActionEvent e)
1783 public void showAllSeqs_actionPerformed(ActionEvent e)
1788 public void showAllColumns_actionPerformed(ActionEvent e)
1793 public void hideSelSequences_actionPerformed(ActionEvent e)
1798 public void hideSelColumns_actionPerformed(ActionEvent e)
1803 public void hiddenMarkers_actionPerformed(ActionEvent e)
1808 public void findPdbId_actionPerformed(ActionEvent e)
1813 public void enterPdbId_actionPerformed(ActionEvent e)
1818 public void pdbFile_actionPerformed(ActionEvent e)
1823 public void invertColSel_actionPerformed(ActionEvent e)
1828 public void tabSelectionChanged(int sel)
1833 public void tabbedPane_mousePressed(MouseEvent e)
1838 public void tabbedPane_focusGained(FocusEvent e)
1843 public void save_actionPerformed(ActionEvent e)
1848 public void reload_actionPerformed(ActionEvent e)
1853 public void newView_actionPerformed(ActionEvent e)
1858 public void textColour_actionPerformed(ActionEvent e)
1863 public void idRightAlign_actionPerformed(ActionEvent e)
1868 public void expandViews_actionPerformed(ActionEvent e)
1873 public void gatherViews_actionPerformed(ActionEvent e)
1878 public void buildTreeMenu()
1883 public void pageSetup_actionPerformed(ActionEvent e)
1888 public void alignmentProperties()