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 JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
150 protected JMenuItem gatherViews = new JMenuItem();
151 protected JMenuItem expandViews = new JMenuItem();
152 JMenuItem pageSetup = new JMenuItem();
153 JMenuItem alignmentProperties = new JMenuItem();
159 setJMenuBar(alignFrameMenuBar);
161 // dynamically fill save as menu with available formats
162 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
164 JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.
165 WRITEABLE_FORMATS[i]);
167 item.addActionListener(new java.awt.event.ActionListener()
169 public void actionPerformed(ActionEvent e)
171 outputText_actionPerformed(e);
175 outputTextboxMenu.add(item);
182 if (!new jalview.util.Platform().isAMac())
184 closeMenuItem.setMnemonic('C');
185 outputTextboxMenu.setMnemonic('T');
186 undoMenuItem.setMnemonic('Z');
187 redoMenuItem.setMnemonic('0');
188 copy.setMnemonic('C');
189 cut.setMnemonic('U');
190 pasteMenu.setMnemonic('P');
191 reload.setMnemonic('R');
194 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
196 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
197 getUserColourSchemes().keys();
199 while (userColours.hasMoreElements())
201 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
203 nextElement().toString());
204 radioItem.setName("USER_DEFINED");
205 radioItem.addMouseListener(new MouseAdapter()
207 public void mousePressed(MouseEvent evt)
209 if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
211 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
213 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
215 "Remove from default list?",
216 "Remove user defined colour",
217 JOptionPane.YES_NO_OPTION);
218 if (option == JOptionPane.YES_OPTION)
220 jalview.gui.UserDefinedColours.removeColourFromDefaults(
221 radioItem.getText());
222 colourMenu.remove(radioItem);
226 radioItem.addActionListener(new ActionListener()
228 public void actionPerformed(ActionEvent evt)
230 userDefinedColour_actionPerformed(evt);
237 radioItem.addActionListener(new ActionListener()
239 public void actionPerformed(ActionEvent evt)
241 userDefinedColour_actionPerformed(evt);
244 colourMenu.insert(radioItem, 15);
245 colours.add(radioItem);
248 colours.add(noColourmenuItem);
249 colours.add(clustalColour);
250 colours.add(zappoColour);
251 colours.add(taylorColour);
252 colours.add(hydrophobicityColour);
253 colours.add(helixColour);
254 colours.add(strandColour);
255 colours.add(turnColour);
256 colours.add(buriedColour);
257 colours.add(userDefinedColour);
258 colours.add(PIDColour);
259 colours.add(BLOSUM62Colour);
260 colours.add(nucleotideColour);
262 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
266 public void setColourSelected(String defaultColour)
269 if (defaultColour != null)
271 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
275 case ColourSchemeProperty.NONE:
276 noColourmenuItem.setSelected(true);
278 case ColourSchemeProperty.CLUSTAL:
279 clustalColour.setSelected(true);
283 case ColourSchemeProperty.BLOSUM:
284 BLOSUM62Colour.setSelected(true);
288 case ColourSchemeProperty.PID:
289 PIDColour.setSelected(true);
293 case ColourSchemeProperty.ZAPPO:
294 zappoColour.setSelected(true);
298 case ColourSchemeProperty.TAYLOR:
299 taylorColour.setSelected(true);
302 case ColourSchemeProperty.HYDROPHOBIC:
303 hydrophobicityColour.setSelected(true);
307 case ColourSchemeProperty.HELIX:
308 helixColour.setSelected(true);
312 case ColourSchemeProperty.STRAND:
313 strandColour.setSelected(true);
317 case ColourSchemeProperty.TURN:
318 turnColour.setSelected(true);
322 case ColourSchemeProperty.BURIED:
323 buriedColour.setSelected(true);
327 case ColourSchemeProperty.NUCLEOTIDE:
328 nucleotideColour.setSelected(true);
332 case ColourSchemeProperty.USER_DEFINED:
333 userDefinedColour.setSelected(true);
341 private void jbInit()
344 fileMenu.setText("File");
345 saveAs.setText("Save As...");
346 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
348 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
349 java.awt.event.KeyEvent.SHIFT_MASK, false));
350 saveAs.addActionListener(new ActionListener()
352 public void actionPerformed(ActionEvent e)
354 saveAs_actionPerformed(e);
357 closeMenuItem.setText("Close");
358 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
359 event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
360 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
362 public void actionPerformed(ActionEvent e)
364 closeMenuItem_actionPerformed(false);
367 editMenu.setText("Edit");
368 viewMenu.setText("View");
369 colourMenu.setText("Colour");
370 calculateMenu.setText("Calculate");
371 webService.setText("Web Service");
372 selectAllSequenceMenuItem.setText("Select All");
373 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
374 java.awt.event.KeyEvent.VK_A,
375 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
376 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
379 public void actionPerformed(ActionEvent e)
381 selectAllSequenceMenuItem_actionPerformed(e);
384 deselectAllSequenceMenuItem.setText("Deselect All");
385 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
387 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
388 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
391 public void actionPerformed(ActionEvent e)
393 deselectAllSequenceMenuItem_actionPerformed(e);
396 invertSequenceMenuItem.setText("Invert Sequence Selection");
397 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
398 java.awt.event.KeyEvent.VK_I,
399 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
400 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
402 public void actionPerformed(ActionEvent e)
404 invertSequenceMenuItem_actionPerformed(e);
407 remove2LeftMenuItem.setText("Remove Left");
408 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
409 awt.event.KeyEvent.VK_L,
410 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
411 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
413 public void actionPerformed(ActionEvent e)
415 remove2LeftMenuItem_actionPerformed(e);
418 remove2RightMenuItem.setText("Remove Right");
419 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
420 awt.event.KeyEvent.VK_R,
421 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
422 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
424 public void actionPerformed(ActionEvent e)
426 remove2RightMenuItem_actionPerformed(e);
429 removeGappedColumnMenuItem.setText("Remove Empty Columns");
430 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
431 getKeyStroke(java.awt.event.
432 KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
433 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
436 public void actionPerformed(ActionEvent e)
438 removeGappedColumnMenuItem_actionPerformed(e);
441 removeAllGapsMenuItem.setText("Remove All Gaps");
442 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
443 java.awt.event.KeyEvent.VK_E,
444 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
445 java.awt.event.KeyEvent.SHIFT_MASK, false));
446 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
448 public void actionPerformed(ActionEvent e)
450 removeAllGapsMenuItem_actionPerformed(e);
453 viewBoxesMenuItem.setText("Boxes");
454 viewBoxesMenuItem.setState(true);
455 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
457 public void actionPerformed(ActionEvent e)
459 viewBoxesMenuItem_actionPerformed(e);
462 viewTextMenuItem.setText("Text");
463 viewTextMenuItem.setState(true);
464 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
466 public void actionPerformed(ActionEvent e)
468 viewTextMenuItem_actionPerformed(e);
471 sortPairwiseMenuItem.setText("by Pairwise Identity");
472 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
474 public void actionPerformed(ActionEvent e)
476 sortPairwiseMenuItem_actionPerformed(e);
479 sortIDMenuItem.setText("by ID");
480 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
482 public void actionPerformed(ActionEvent e)
484 sortIDMenuItem_actionPerformed(e);
487 sortGroupMenuItem.setText("by Group");
488 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
490 public void actionPerformed(ActionEvent e)
492 sortGroupMenuItem_actionPerformed(e);
495 removeRedundancyMenuItem.setText("Remove Redundancy...");
496 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
497 java.awt.event.KeyEvent.VK_D,
498 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
499 removeRedundancyMenuItem.addActionListener(new java.awt.event.
502 public void actionPerformed(ActionEvent e)
504 removeRedundancyMenuItem_actionPerformed(e);
507 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
508 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
511 public void actionPerformed(ActionEvent e)
513 pairwiseAlignmentMenuItem_actionPerformed(e);
516 PCAMenuItem.setText("Principal Component Analysis");
517 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
519 public void actionPerformed(ActionEvent e)
521 PCAMenuItem_actionPerformed(e);
524 averageDistanceTreeMenuItem.setText(
525 "Average Distance Using % Identity");
526 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
529 public void actionPerformed(ActionEvent e)
531 averageDistanceTreeMenuItem_actionPerformed(e);
534 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
535 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
537 public void actionPerformed(ActionEvent e)
539 neighbourTreeMenuItem_actionPerformed(e);
542 this.getContentPane().setLayout(borderLayout1);
543 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
544 statusBar.setBackground(Color.white);
545 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
546 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
547 statusBar.setText("Status bar");
548 outputTextboxMenu.setText("Output to Textbox");
549 clustalColour.setText("Clustalx");
551 clustalColour.addActionListener(new java.awt.event.ActionListener()
553 public void actionPerformed(ActionEvent e)
555 clustalColour_actionPerformed(e);
558 zappoColour.setText("Zappo");
559 zappoColour.addActionListener(new java.awt.event.ActionListener()
561 public void actionPerformed(ActionEvent e)
563 zappoColour_actionPerformed(e);
566 taylorColour.setText("Taylor");
567 taylorColour.addActionListener(new java.awt.event.ActionListener()
569 public void actionPerformed(ActionEvent e)
571 taylorColour_actionPerformed(e);
574 hydrophobicityColour.setText("Hydrophobicity");
575 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
577 public void actionPerformed(ActionEvent e)
579 hydrophobicityColour_actionPerformed(e);
582 helixColour.setText("Helix Propensity");
583 helixColour.addActionListener(new java.awt.event.ActionListener()
585 public void actionPerformed(ActionEvent e)
587 helixColour_actionPerformed(e);
590 strandColour.setText("Strand Propensity");
591 strandColour.addActionListener(new java.awt.event.ActionListener()
593 public void actionPerformed(ActionEvent e)
595 strandColour_actionPerformed(e);
598 turnColour.setText("Turn Propensity");
599 turnColour.addActionListener(new java.awt.event.ActionListener()
601 public void actionPerformed(ActionEvent e)
603 turnColour_actionPerformed(e);
606 buriedColour.setText("Buried Index");
607 buriedColour.addActionListener(new java.awt.event.ActionListener()
609 public void actionPerformed(ActionEvent e)
611 buriedColour_actionPerformed(e);
614 userDefinedColour.setText("User Defined...");
615 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
617 public void actionPerformed(ActionEvent e)
619 userDefinedColour_actionPerformed(e);
622 PIDColour.setText("Percentage Identity");
623 PIDColour.addActionListener(new java.awt.event.ActionListener()
625 public void actionPerformed(ActionEvent e)
627 PIDColour_actionPerformed(e);
630 BLOSUM62Colour.setText("BLOSUM62 Score");
631 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
633 public void actionPerformed(ActionEvent e)
635 BLOSUM62Colour_actionPerformed(e);
638 avDistanceTreeBlosumMenuItem.setText(
639 "Average Distance Using BLOSUM62");
640 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
643 public void actionPerformed(ActionEvent e)
645 avTreeBlosumMenuItem_actionPerformed(e);
648 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
649 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
651 public void actionPerformed(ActionEvent e)
653 njTreeBlosumMenuItem_actionPerformed(e);
656 annotationPanelMenuItem.setActionCommand("");
657 annotationPanelMenuItem.setText("Show Annotations");
658 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
659 "SHOW_ANNOTATIONS", true));
660 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
662 public void actionPerformed(ActionEvent e)
664 annotationPanelMenuItem_actionPerformed(e);
667 colourTextMenuItem.setText("Colour Text");
668 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
670 public void actionPerformed(ActionEvent e)
672 colourTextMenuItem_actionPerformed(e);
675 htmlMenuItem.setText("HTML");
676 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
678 public void actionPerformed(ActionEvent e)
680 htmlMenuItem_actionPerformed(e);
683 overviewMenuItem.setText("Overview Window");
684 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
686 public void actionPerformed(ActionEvent e)
688 overviewMenuItem_actionPerformed(e);
691 undoMenuItem.setEnabled(false);
692 undoMenuItem.setText("Undo");
693 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
694 java.awt.event.KeyEvent.VK_Z,
695 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
696 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
698 public void actionPerformed(ActionEvent e)
700 undoMenuItem_actionPerformed(e);
703 redoMenuItem.setEnabled(false);
704 redoMenuItem.setText("Redo");
705 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
706 event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
707 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
709 public void actionPerformed(ActionEvent e)
711 redoMenuItem_actionPerformed(e);
714 conservationMenuItem.setText("By Conservation");
715 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
717 public void actionPerformed(ActionEvent e)
719 conservationMenuItem_actionPerformed(e);
722 noColourmenuItem.setText("None");
723 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
725 public void actionPerformed(ActionEvent e)
727 noColourmenuItem_actionPerformed(e);
730 wrapMenuItem.setText("Wrap");
731 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
733 public void actionPerformed(ActionEvent e)
735 wrapMenuItem_actionPerformed(e);
738 printMenuItem.setText("Print ...");
739 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
740 event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
741 printMenuItem.addActionListener(new java.awt.event.ActionListener()
743 public void actionPerformed(ActionEvent e)
745 printMenuItem_actionPerformed(e);
748 renderGapsMenuItem.setText("Show Gaps");
749 renderGapsMenuItem.setState(true);
750 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
752 public void actionPerformed(ActionEvent e)
754 renderGapsMenuItem_actionPerformed(e);
757 findMenuItem.setText("Find...");
758 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
759 java.awt.event.KeyEvent.VK_F,
760 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
761 findMenuItem.addActionListener(new java.awt.event.ActionListener()
763 public void actionPerformed(ActionEvent e)
765 findMenuItem_actionPerformed(e);
768 abovePIDThreshold.setText("Above Identity Threshold");
769 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
771 public void actionPerformed(ActionEvent e)
773 abovePIDThreshold_actionPerformed(e);
776 showSeqFeatures.setText("Show Sequence Features");
777 showSeqFeatures.addActionListener(new ActionListener()
779 public void actionPerformed(ActionEvent actionEvent)
781 showSeqFeatures_actionPerformed(actionEvent);
784 nucleotideColour.setText("Nucleotide");
785 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
787 public void actionPerformed(ActionEvent e)
789 nucleotideColour_actionPerformed(e);
792 deleteGroups.setText("Undefine groups");
793 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
794 event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
795 deleteGroups.addActionListener(new java.awt.event.ActionListener()
797 public void actionPerformed(ActionEvent e)
799 deleteGroups_actionPerformed(e);
802 copy.setText("Copy");
803 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
804 java.awt.event.KeyEvent.VK_C,
805 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
807 copy.addActionListener(new java.awt.event.ActionListener()
809 public void actionPerformed(ActionEvent e)
811 copy_actionPerformed(e);
815 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
816 java.awt.event.KeyEvent.VK_X,
817 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
818 cut.addActionListener(new java.awt.event.ActionListener()
820 public void actionPerformed(ActionEvent e)
822 cut_actionPerformed(e);
825 delete.setText("Delete");
826 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
827 KeyEvent.VK_BACK_SPACE, 0, false));
828 delete.addActionListener(new java.awt.event.ActionListener()
830 public void actionPerformed(ActionEvent e)
832 delete_actionPerformed(e);
835 pasteMenu.setText("Paste");
836 pasteNew.setText("To New Alignment");
837 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
838 java.awt.event.KeyEvent.VK_V,
839 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
840 java.awt.event.KeyEvent.SHIFT_MASK, false));
841 pasteNew.addActionListener(new java.awt.event.ActionListener()
843 public void actionPerformed(ActionEvent e)
845 pasteNew_actionPerformed(e);
848 pasteThis.setText("Add To This Alignment");
849 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
850 java.awt.event.KeyEvent.VK_V,
851 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
852 pasteThis.addActionListener(new java.awt.event.ActionListener()
854 public void actionPerformed(ActionEvent e)
856 pasteThis_actionPerformed(e);
859 applyToAllGroups.setText("Apply Colour To All Groups");
860 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
862 public void actionPerformed(ActionEvent e)
864 applyToAllGroups_actionPerformed(e);
867 createPNG.addActionListener(new java.awt.event.ActionListener()
869 public void actionPerformed(ActionEvent e)
874 createPNG.setActionCommand("Save As PNG Image");
875 createPNG.setText("PNG");
876 font.setText("Font...");
877 font.addActionListener(new java.awt.event.ActionListener()
879 public void actionPerformed(ActionEvent e)
881 font_actionPerformed(e);
885 seqLimits.setText("Show Sequence Limits");
886 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
887 seqLimits.addActionListener(new java.awt.event.ActionListener()
889 public void actionPerformed(ActionEvent e)
891 seqLimit_actionPerformed(e);
894 epsFile.setText("EPS");
895 epsFile.addActionListener(new java.awt.event.ActionListener()
897 public void actionPerformed(ActionEvent e)
902 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
903 LoadtreeMenuItem.setText("Load Associated Tree");
904 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
906 public void actionPerformed(ActionEvent e)
908 LoadtreeMenuItem_actionPerformed(e);
911 scaleAbove.setVisible(false);
912 scaleAbove.setText("Scale Above");
913 scaleAbove.addActionListener(new java.awt.event.ActionListener()
915 public void actionPerformed(ActionEvent e)
917 scaleAbove_actionPerformed(e);
920 scaleLeft.setVisible(false);
921 scaleLeft.setSelected(true);
922 scaleLeft.setText("Scale Left");
923 scaleLeft.addActionListener(new java.awt.event.ActionListener()
925 public void actionPerformed(ActionEvent e)
927 scaleLeft_actionPerformed(e);
930 scaleRight.setVisible(false);
931 scaleRight.setSelected(true);
932 scaleRight.setText("Scale Right");
933 scaleRight.addActionListener(new java.awt.event.ActionListener()
935 public void actionPerformed(ActionEvent e)
937 scaleRight_actionPerformed(e);
940 centreColumnLabelsMenuItem.setVisible(true);
941 centreColumnLabelsMenuItem.setState(false);
942 centreColumnLabelsMenuItem.setText("Centre Column Labels");
943 centreColumnLabelsMenuItem.addActionListener(new java.awt.event.ActionListener()
945 public void actionPerformed(ActionEvent e)
947 centreColumnLabels_actionPerformed(e);
951 modifyPID.setText("Modify Identity Threshold...");
952 modifyPID.addActionListener(new java.awt.event.ActionListener()
954 public void actionPerformed(ActionEvent e)
956 modifyPID_actionPerformed(e);
959 modifyConservation.setText("Modify Conservation Threshold...");
960 modifyConservation.addActionListener(new java.awt.event.ActionListener()
962 public void actionPerformed(ActionEvent e)
964 modifyConservation_actionPerformed(e);
967 sortByTreeMenu.setText("By Tree Order");
968 sort.setText("Sort");
969 sort.addMenuListener(new MenuListener()
971 public void menuSelected(MenuEvent e)
976 public void menuDeselected(MenuEvent e)
980 public void menuCanceled(MenuEvent e)
984 sortByAnnotScore.setText("by Score");
985 sort.add(sortByAnnotScore);
986 sortByAnnotScore.addMenuListener(
987 new javax.swing.event.MenuListener() {
989 public void menuCanceled(MenuEvent e)
993 public void menuDeselected(MenuEvent e)
997 public void menuSelected(MenuEvent e)
999 buildSortByAnnotationScoresMenu();
1003 sortByAnnotScore.setVisible(false);
1005 calculate.setText("Calculate Tree");
1007 jMenu2.setText("Export Image");
1008 padGapsMenuitem.setText("Pad Gaps");
1009 padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1010 padGapsMenuitem.addActionListener(new ActionListener()
1012 public void actionPerformed(ActionEvent e)
1014 padGapsMenuitem_actionPerformed(e);
1017 vamsasStore.setVisible(false);
1018 vamsasStore.setText("VAMSAS store");
1019 vamsasStore.addActionListener(new ActionListener()
1021 public void actionPerformed(ActionEvent e)
1023 vamsasStore_actionPerformed(e);
1026 showTranslation.setText("Translate cDNA");
1027 showTranslation.addActionListener(new ActionListener()
1029 public void actionPerformed(ActionEvent e)
1031 showTranslation_actionPerformed(e);
1034 extractScores.setText("Extract Scores...");
1035 extractScores.addActionListener(new ActionListener()
1037 public void actionPerformed(ActionEvent e)
1039 extractScores_actionPerformed(e);
1042 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based score extraction
1043 showProducts.setText("Get Cross References");
1044 /*showProducts.addActionListener(new ActionListener()
1047 public void actionPerformed(ActionEvent e)
1049 showProducts_actionPerformed(e);
1052 featureSettings.setText("Feature Settings...");
1053 featureSettings.addActionListener(new ActionListener()
1055 public void actionPerformed(ActionEvent e)
1057 featureSettings_actionPerformed(e);
1060 fetchSequence.setText("Fetch Sequence(s)...");
1061 fetchSequence.addActionListener(new ActionListener()
1063 public void actionPerformed(ActionEvent e)
1065 fetchSequence_actionPerformed(e);
1069 annotationColour.setText("By Annotation...");
1070 annotationColour.addActionListener(new ActionListener()
1072 public void actionPerformed(ActionEvent e)
1074 annotationColour_actionPerformed(e);
1077 associatedData.setText("Load Features / Annotations");
1078 associatedData.addActionListener(new ActionListener()
1080 public void actionPerformed(ActionEvent e)
1082 associatedData_actionPerformed(e);
1085 autoCalculate.setText("Autocalculate Consensus");
1086 autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1087 autoCalculate.addActionListener(new ActionListener()
1089 public void actionPerformed(ActionEvent e)
1091 autoCalculate_actionPerformed(e);
1094 addSequenceMenu.setText("Add Sequences");
1095 addFromFile.setText("From File");
1096 addFromFile.addActionListener(new ActionListener()
1098 public void actionPerformed(ActionEvent e)
1100 addFromFile_actionPerformed(e);
1103 addFromText.setText("From Textbox");
1104 addFromText.addActionListener(new ActionListener()
1106 public void actionPerformed(ActionEvent e)
1108 addFromText_actionPerformed(e);
1111 addFromURL.setText("From URL");
1112 addFromURL.addActionListener(new ActionListener()
1114 public void actionPerformed(ActionEvent e)
1116 addFromURL_actionPerformed(e);
1119 exportFeatures.setText("Export Features...");
1120 exportFeatures.addActionListener(new ActionListener()
1122 public void actionPerformed(ActionEvent e)
1124 exportFeatures_actionPerformed(e);
1127 exportAnnotations.setText("Export Annotations...");
1128 exportAnnotations.addActionListener(new ActionListener()
1130 public void actionPerformed(ActionEvent e)
1132 exportAnnotations_actionPerformed(e);
1135 statusPanel.setLayout(gridLayout1);
1136 jMenu3.setText("Show");
1137 showAllSeqs.setText("All Sequences");
1138 showAllSeqs.addActionListener(new ActionListener()
1140 public void actionPerformed(ActionEvent e)
1142 showAllSeqs_actionPerformed(e);
1145 showAllColumns.setText("All Columns");
1146 showAllColumns.addActionListener(new ActionListener()
1148 public void actionPerformed(ActionEvent e)
1150 showAllColumns_actionPerformed(e);
1153 hideMenu.setText("Hide");
1154 hideSelSequences.setText("Selected Sequences");
1155 hideSelSequences.addActionListener(new ActionListener()
1157 public void actionPerformed(ActionEvent e)
1159 hideSelSequences_actionPerformed(e);
1162 hideSelColumns.setText("Selected Columns");
1163 hideSelColumns.addActionListener(new ActionListener()
1165 public void actionPerformed(ActionEvent e)
1167 hideSelColumns_actionPerformed(e);
1170 hiddenMarkers.setText("Show Hidden Markers");
1171 hiddenMarkers.addActionListener(new ActionListener()
1173 public void actionPerformed(ActionEvent e)
1175 hiddenMarkers_actionPerformed(e);
1178 invertColSel.setText("Invert Column Selection");
1179 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
1180 event.KeyEvent.VK_I,
1181 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1182 | java.awt.event.KeyEvent.ALT_MASK,
1184 invertColSel.addActionListener(new ActionListener()
1186 public void actionPerformed(ActionEvent e)
1188 invertColSel_actionPerformed(e);
1191 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1193 public void stateChanged(ChangeEvent evt)
1195 JTabbedPane pane = (JTabbedPane) evt.getSource();
1196 int sel = pane.getSelectedIndex();
1197 tabSelectionChanged(sel);
1200 tabbedPane.addMouseListener(new MouseAdapter()
1202 public void mousePressed(MouseEvent e)
1204 tabbedPane_mousePressed(e);
1207 tabbedPane.addFocusListener(new FocusAdapter()
1209 public void focusGained(FocusEvent e)
1211 tabbedPane_focusGained(e);
1214 save.setText("Save");
1215 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
1216 KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
1217 save.addActionListener(new ActionListener()
1219 public void actionPerformed(ActionEvent e)
1221 save_actionPerformed(e);
1224 reload.setEnabled(false);
1225 reload.setText("Reload");
1226 reload.addActionListener(new ActionListener()
1228 public void actionPerformed(ActionEvent e)
1230 reload_actionPerformed(e);
1233 newView.setText("New View");
1234 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
1235 KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
1236 newView.addActionListener(new ActionListener()
1238 public void actionPerformed(ActionEvent e)
1240 newView_actionPerformed(e);
1243 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1245 "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1246 textColour.setText("Colour Text ...");
1247 textColour.addActionListener(new ActionListener()
1249 public void actionPerformed(ActionEvent e)
1251 textColour_actionPerformed(e);
1254 formatMenu.setText("Format");
1255 selectMenu.setText("Select");
1256 idRightAlign.setText("Right Align Sequence Id");
1257 idRightAlign.addActionListener(new ActionListener()
1259 public void actionPerformed(ActionEvent e)
1261 idRightAlign_actionPerformed(e);
1264 gatherViews.setEnabled(false);
1265 gatherViews.setText("Gather Views");
1266 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
1267 event.KeyEvent.VK_G, 0, false));
1268 gatherViews.addActionListener(new ActionListener()
1270 public void actionPerformed(ActionEvent e)
1272 gatherViews_actionPerformed(e);
1275 expandViews.setEnabled(false);
1276 expandViews.setText("Expand Views");
1277 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
1278 event.KeyEvent.VK_X, 0, false));
1279 expandViews.addActionListener(new ActionListener()
1281 public void actionPerformed(ActionEvent e)
1283 expandViews_actionPerformed(e);
1286 pageSetup.setText("Page Setup ...");
1287 pageSetup.addActionListener(new ActionListener()
1289 public void actionPerformed(ActionEvent e)
1291 pageSetup_actionPerformed(e);
1294 alignmentProperties.setText("Alignment Properties...");
1295 alignmentProperties.addActionListener(new ActionListener()
1297 public void actionPerformed(ActionEvent actionEvent)
1299 alignmentProperties();
1303 alignFrameMenuBar.add(fileMenu);
1304 alignFrameMenuBar.add(editMenu);
1305 alignFrameMenuBar.add(selectMenu);
1306 alignFrameMenuBar.add(viewMenu);
1307 alignFrameMenuBar.add(formatMenu);
1308 alignFrameMenuBar.add(colourMenu);
1309 alignFrameMenuBar.add(calculateMenu);
1310 alignFrameMenuBar.add(webService);
1311 fileMenu.add(fetchSequence);
1312 fileMenu.add(addSequenceMenu);
1313 fileMenu.add(reload);
1314 fileMenu.addSeparator();
1315 fileMenu.add(vamsasStore);
1317 fileMenu.add(saveAs);
1318 fileMenu.add(outputTextboxMenu);
1319 fileMenu.add(pageSetup);
1320 fileMenu.add(printMenuItem);
1321 fileMenu.addSeparator();
1322 fileMenu.add(jMenu2);
1323 fileMenu.add(exportFeatures);
1324 fileMenu.add(exportAnnotations);
1325 fileMenu.add(LoadtreeMenuItem);
1326 fileMenu.add(associatedData);
1327 fileMenu.addSeparator();
1328 fileMenu.add(closeMenuItem);
1329 editMenu.add(undoMenuItem);
1330 editMenu.add(redoMenuItem);
1333 editMenu.add(pasteMenu);
1334 editMenu.add(delete);
1335 editMenu.addSeparator();
1336 editMenu.add(remove2LeftMenuItem);
1337 editMenu.add(remove2RightMenuItem);
1338 editMenu.add(removeGappedColumnMenuItem);
1339 editMenu.add(removeAllGapsMenuItem);
1340 editMenu.add(removeRedundancyMenuItem);
1341 editMenu.addSeparator();
1342 editMenu.add(padGapsMenuitem);
1343 viewMenu.add(newView);
1344 viewMenu.add(expandViews);
1345 viewMenu.add(gatherViews);
1346 viewMenu.addSeparator();
1347 viewMenu.add(jMenu3);
1348 viewMenu.add(hideMenu);
1349 viewMenu.addSeparator();
1350 viewMenu.add(annotationPanelMenuItem);
1351 viewMenu.addSeparator();
1352 viewMenu.add(showSeqFeatures);
1353 viewMenu.add(featureSettings);
1354 viewMenu.addSeparator();
1355 viewMenu.add(alignmentProperties);
1356 viewMenu.addSeparator();
1357 viewMenu.add(overviewMenuItem);
1358 colourMenu.add(applyToAllGroups);
1359 colourMenu.add(textColour);
1360 colourMenu.addSeparator();
1361 colourMenu.add(noColourmenuItem);
1362 colourMenu.add(clustalColour);
1363 colourMenu.add(BLOSUM62Colour);
1364 colourMenu.add(PIDColour);
1365 colourMenu.add(zappoColour);
1366 colourMenu.add(taylorColour);
1367 colourMenu.add(hydrophobicityColour);
1368 colourMenu.add(helixColour);
1369 colourMenu.add(strandColour);
1370 colourMenu.add(turnColour);
1371 colourMenu.add(buriedColour);
1372 colourMenu.add(nucleotideColour);
1373 colourMenu.add(userDefinedColour);
1374 colourMenu.addSeparator();
1375 colourMenu.add(conservationMenuItem);
1376 colourMenu.add(modifyConservation);
1377 colourMenu.add(abovePIDThreshold);
1378 colourMenu.add(modifyPID);
1379 colourMenu.add(annotationColour);
1380 calculateMenu.add(sort);
1381 calculateMenu.add(calculate);
1382 calculateMenu.addSeparator();
1383 calculateMenu.add(pairwiseAlignmentMenuItem);
1384 calculateMenu.add(PCAMenuItem);
1385 calculateMenu.addSeparator();
1386 calculateMenu.add(showTranslation);
1387 calculateMenu.add(showProducts);
1388 calculateMenu.add(autoCalculate);
1389 calculateMenu.addSeparator();
1390 calculateMenu.add(extractScores);
1391 webServiceNoServices = new JMenuItem("<No Services>");
1392 webService.add(webServiceNoServices);
1393 pasteMenu.add(pasteNew);
1394 pasteMenu.add(pasteThis);
1395 sort.add(sortIDMenuItem);
1396 sort.add(sortGroupMenuItem);
1397 sort.add(sortPairwiseMenuItem);
1398 sort.add(sortByTreeMenu);
1399 calculate.add(averageDistanceTreeMenuItem);
1400 calculate.add(neighbourTreeMenuItem);
1401 calculate.add(avDistanceTreeBlosumMenuItem);
1402 calculate.add(njTreeBlosumMenuItem);
1403 jMenu2.add(htmlMenuItem);
1404 jMenu2.add(epsFile);
1405 jMenu2.add(createPNG);
1406 addSequenceMenu.add(addFromFile);
1407 addSequenceMenu.add(addFromText);
1408 addSequenceMenu.add(addFromURL);
1409 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1410 statusPanel.add(statusBar, null);
1411 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1412 jMenu3.add(showAllColumns);
1413 jMenu3.add(showAllSeqs);
1414 hideMenu.add(hideSelColumns);
1415 hideMenu.add(hideSelSequences);
1416 formatMenu.add(font);
1417 formatMenu.addSeparator();
1418 formatMenu.add(wrapMenuItem);
1419 formatMenu.add(scaleAbove);
1420 formatMenu.add(scaleLeft);
1421 formatMenu.add(scaleRight);
1422 formatMenu.add(seqLimits);
1423 formatMenu.add(idRightAlign);
1424 formatMenu.add(hiddenMarkers);
1425 formatMenu.add(viewBoxesMenuItem);
1426 formatMenu.add(viewTextMenuItem);
1427 formatMenu.add(colourTextMenuItem);
1428 formatMenu.add(renderGapsMenuItem);
1429 formatMenu.add(centreColumnLabelsMenuItem);
1430 selectMenu.add(findMenuItem);
1431 selectMenu.addSeparator();
1432 selectMenu.add(selectAllSequenceMenuItem);
1433 selectMenu.add(deselectAllSequenceMenuItem);
1434 selectMenu.add(invertSequenceMenuItem);
1435 selectMenu.add(invertColSel);
1436 selectMenu.add(deleteGroups);
1439 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1443 protected void showProducts_actionPerformed(ActionEvent e)
1447 protected void buildSortByAnnotationScoresMenu()
1451 protected void extractScores_actionPerformed(ActionEvent e)
1455 protected void outputText_actionPerformed(ActionEvent e)
1459 public void addFromFile_actionPerformed(ActionEvent e)
1464 public void addFromText_actionPerformed(ActionEvent e)
1469 public void addFromURL_actionPerformed(ActionEvent e)
1474 public void exportFeatures_actionPerformed(ActionEvent e)
1479 public void exportAnnotations_actionPerformed(ActionEvent e)
1484 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1488 protected void closeMenuItem_actionPerformed(boolean b)
1492 protected void redoMenuItem_actionPerformed(ActionEvent e)
1496 protected void undoMenuItem_actionPerformed(ActionEvent e)
1500 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1504 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1508 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1512 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1516 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1520 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1524 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1528 protected void wrapMenuItem_actionPerformed(ActionEvent e)
1532 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1536 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1540 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1544 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1548 protected void overviewMenuItem_actionPerformed(ActionEvent e)
1552 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1556 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1560 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1564 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1568 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1572 protected void PCAMenuItem_actionPerformed(ActionEvent e)
1576 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1580 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1584 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1588 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1592 protected void clustalColour_actionPerformed(ActionEvent e)
1596 protected void zappoColour_actionPerformed(ActionEvent e)
1600 protected void taylorColour_actionPerformed(ActionEvent e)
1604 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1608 protected void helixColour_actionPerformed(ActionEvent e)
1612 protected void strandColour_actionPerformed(ActionEvent e)
1616 protected void turnColour_actionPerformed(ActionEvent e)
1620 protected void buriedColour_actionPerformed(ActionEvent e)
1624 protected void userDefinedColour_actionPerformed(ActionEvent e)
1628 protected void PIDColour_actionPerformed(ActionEvent e)
1632 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1636 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1640 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1644 protected void printMenuItem_actionPerformed(ActionEvent e)
1648 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1652 protected void findMenuItem_actionPerformed(ActionEvent e)
1656 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1660 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
1664 protected void nucleotideColour_actionPerformed(ActionEvent e)
1668 protected void deleteGroups_actionPerformed(ActionEvent e)
1672 protected void copy_actionPerformed(ActionEvent e)
1676 protected void cut_actionPerformed(ActionEvent e)
1680 protected void delete_actionPerformed(ActionEvent e)
1684 protected void pasteNew_actionPerformed(ActionEvent e)
1688 protected void pasteThis_actionPerformed(ActionEvent e)
1692 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1696 public void createPNG(java.io.File f)
1700 protected void font_actionPerformed(ActionEvent e)
1704 protected void seqLimit_actionPerformed(ActionEvent e)
1708 public void seqDBRef_actionPerformed(ActionEvent e)
1713 public void createEPS(java.io.File f)
1717 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
1721 protected void jpred_actionPerformed(ActionEvent e)
1725 protected void scaleAbove_actionPerformed(ActionEvent e)
1729 protected void scaleLeft_actionPerformed(ActionEvent e)
1733 protected void scaleRight_actionPerformed(ActionEvent e)
1737 protected void modifyPID_actionPerformed(ActionEvent e)
1741 protected void modifyConservation_actionPerformed(ActionEvent e)
1745 protected void saveAs_actionPerformed(ActionEvent e)
1749 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
1753 public void vamsasStore_actionPerformed(ActionEvent e)
1758 public void vamsasLoad_actionPerformed(ActionEvent e)
1763 public void showTranslation_actionPerformed(ActionEvent e)
1768 public void featureSettings_actionPerformed(ActionEvent e)
1773 public void fetchSequence_actionPerformed(ActionEvent e)
1778 public void smoothFont_actionPerformed(ActionEvent e)
1783 public void annotationColour_actionPerformed(ActionEvent e)
1788 public void associatedData_actionPerformed(ActionEvent e)
1793 public void autoCalculate_actionPerformed(ActionEvent e)
1798 public void showAllSeqs_actionPerformed(ActionEvent e)
1803 public void showAllColumns_actionPerformed(ActionEvent e)
1808 public void hideSelSequences_actionPerformed(ActionEvent e)
1813 public void hideSelColumns_actionPerformed(ActionEvent e)
1818 public void hiddenMarkers_actionPerformed(ActionEvent e)
1823 public void findPdbId_actionPerformed(ActionEvent e)
1828 public void enterPdbId_actionPerformed(ActionEvent e)
1833 public void pdbFile_actionPerformed(ActionEvent e)
1838 public void invertColSel_actionPerformed(ActionEvent e)
1843 public void tabSelectionChanged(int sel)
1848 public void tabbedPane_mousePressed(MouseEvent e)
1853 public void tabbedPane_focusGained(FocusEvent e)
1858 public void save_actionPerformed(ActionEvent e)
1863 public void reload_actionPerformed(ActionEvent e)
1868 public void newView_actionPerformed(ActionEvent e)
1873 public void textColour_actionPerformed(ActionEvent e)
1878 public void idRightAlign_actionPerformed(ActionEvent e)
1883 public void expandViews_actionPerformed(ActionEvent e)
1888 public void gatherViews_actionPerformed(ActionEvent e)
1893 public void buildTreeMenu()
1898 public void pageSetup_actionPerformed(ActionEvent e)
1903 public void alignmentProperties()