2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 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 extends JInternalFrame
31 protected JMenuBar alignFrameMenuBar = new JMenuBar();
33 protected JMenu fileMenu = new JMenu();
35 protected JMenuItem closeMenuItem = new JMenuItem();
37 protected JMenu editMenu = new JMenu();
39 protected JMenu viewMenu = new JMenu();
41 protected JMenu colourMenu = new JMenu();
43 protected JMenu calculateMenu = new JMenu();
45 protected JMenu webService = new JMenu();
47 protected JMenuItem webServiceNoServices;
49 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
51 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
53 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
55 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
57 protected JMenuItem remove2RightMenuItem = new JMenuItem();
59 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
61 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
63 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
65 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
67 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
69 protected JMenuItem sortIDMenuItem = new JMenuItem();
71 protected JMenuItem sortGroupMenuItem = new JMenuItem();
73 protected JMenu sortByAnnotScore = new JMenu();
75 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
77 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
79 protected JMenuItem PCAMenuItem = new JMenuItem();
81 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
83 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
85 BorderLayout borderLayout1 = new BorderLayout();
87 public JLabel statusBar = new JLabel();
89 protected JMenuItem saveAs = new JMenuItem();
91 protected JMenu outputTextboxMenu = new JMenu();
93 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
95 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
97 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
99 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
101 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
103 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
105 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
107 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
109 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
111 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
113 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
115 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
117 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
119 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
121 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
123 JMenuItem htmlMenuItem = new JMenuItem();
125 JMenuItem overviewMenuItem = new JMenuItem();
127 protected JMenuItem undoMenuItem = new JMenuItem();
129 protected JMenuItem redoMenuItem = new JMenuItem();
131 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
133 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
135 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
137 JMenuItem printMenuItem = new JMenuItem();
139 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
141 JMenuItem findMenuItem = new JMenuItem();
143 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
145 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
147 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
149 JMenuItem deleteGroups = new JMenuItem();
151 JMenuItem delete = new JMenuItem();
153 JMenuItem copy = new JMenuItem();
155 JMenuItem cut = new JMenuItem();
157 JMenu pasteMenu = new JMenu();
159 JMenuItem pasteNew = new JMenuItem();
161 JMenuItem pasteThis = new JMenuItem();
163 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
165 JMenuItem createPNG = new JMenuItem();
167 protected JMenuItem font = new JMenuItem();
169 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
171 JMenuItem epsFile = new JMenuItem();
173 JMenuItem LoadtreeMenuItem = new JMenuItem();
175 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
177 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
179 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
181 protected JMenuItem modifyPID = new JMenuItem();
183 protected JMenuItem modifyConservation = new JMenuItem();
185 protected JMenu sortByTreeMenu = new JMenu();
187 protected JMenu sort = new JMenu();
189 JMenu calculate = new JMenu();
191 JMenu jMenu2 = new JMenu();
193 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
194 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
195 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
197 protected ButtonGroup colours = new ButtonGroup();
199 JMenuItem vamsasStore = new JMenuItem();
201 protected JMenuItem showTranslation = new JMenuItem();
203 protected JMenuItem extractScores = new JMenuItem();
205 protected JMenu showProducts = new JMenu();
207 public JMenuItem featureSettings = new JMenuItem();
209 JMenuItem fetchSequence = new JMenuItem();
211 JMenuItem annotationColour = new JMenuItem();
213 JMenuItem associatedData = new JMenuItem();
215 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
217 JMenu addSequenceMenu = new JMenu();
219 JMenuItem addFromFile = new JMenuItem();
221 JMenuItem addFromText = new JMenuItem();
223 JMenuItem addFromURL = new JMenuItem();
225 JMenuItem exportAnnotations = new JMenuItem();
227 JMenuItem exportFeatures = new JMenuItem();
229 protected JPanel statusPanel = new JPanel();
231 GridLayout gridLayout1 = new GridLayout();
233 JMenu jMenu3 = new JMenu();
235 JMenuItem showAllSeqs = new JMenuItem();
237 JMenuItem showAllColumns = new JMenuItem();
239 JMenu hideMenu = new JMenu();
241 JMenuItem hideSelSequences = new JMenuItem();
243 JMenuItem hideSelColumns = new JMenuItem();
245 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
247 JMenuItem invertColSel = new JMenuItem();
249 protected JTabbedPane tabbedPane = new JTabbedPane();
251 JMenuItem save = new JMenuItem();
253 protected JMenuItem reload = new JMenuItem();
255 JMenuItem newView = new JMenuItem();
257 JMenuItem textColour = new JMenuItem();
259 JMenu formatMenu = new JMenu();
261 JMenu selectMenu = new JMenu();
263 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
265 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
267 protected JMenuItem gatherViews = new JMenuItem();
269 protected JMenuItem expandViews = new JMenuItem();
271 JMenuItem pageSetup = new JMenuItem();
273 JMenuItem alignmentProperties = new JMenuItem();
275 JMenu tooltipSettingsMenu = new JMenu();
282 setJMenuBar(alignFrameMenuBar);
284 // dynamically fill save as menu with available formats
285 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
287 JMenuItem item = new JMenuItem(
288 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
290 item.addActionListener(new java.awt.event.ActionListener()
292 public void actionPerformed(ActionEvent e)
294 outputText_actionPerformed(e);
298 outputTextboxMenu.add(item);
300 } catch (Exception e)
304 if (!new jalview.util.Platform().isAMac())
306 closeMenuItem.setMnemonic('C');
307 outputTextboxMenu.setMnemonic('T');
308 undoMenuItem.setMnemonic('Z');
309 redoMenuItem.setMnemonic('0');
310 copy.setMnemonic('C');
311 cut.setMnemonic('U');
312 pasteMenu.setMnemonic('P');
313 reload.setMnemonic('R');
316 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
318 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
319 .getUserColourSchemes().keys();
321 while (userColours.hasMoreElements())
323 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
324 userColours.nextElement().toString());
325 radioItem.setName("USER_DEFINED");
326 radioItem.addMouseListener(new MouseAdapter()
328 public void mousePressed(MouseEvent evt)
330 if (evt.isControlDown()
331 || SwingUtilities.isRightMouseButton(evt))
334 .removeActionListener(radioItem.getActionListeners()[0]);
336 int option = JOptionPane.showInternalConfirmDialog(
337 jalview.gui.Desktop.desktop,
338 "Remove from default list?",
339 "Remove user defined colour",
340 JOptionPane.YES_NO_OPTION);
341 if (option == JOptionPane.YES_OPTION)
343 jalview.gui.UserDefinedColours
344 .removeColourFromDefaults(radioItem.getText());
345 colourMenu.remove(radioItem);
349 radioItem.addActionListener(new ActionListener()
351 public void actionPerformed(ActionEvent evt)
353 userDefinedColour_actionPerformed(evt);
360 radioItem.addActionListener(new ActionListener()
362 public void actionPerformed(ActionEvent evt)
364 userDefinedColour_actionPerformed(evt);
367 colourMenu.insert(radioItem, 15);
368 colours.add(radioItem);
371 colours.add(noColourmenuItem);
372 colours.add(clustalColour);
373 colours.add(zappoColour);
374 colours.add(taylorColour);
375 colours.add(hydrophobicityColour);
376 colours.add(helixColour);
377 colours.add(strandColour);
378 colours.add(turnColour);
379 colours.add(buriedColour);
380 colours.add(userDefinedColour);
381 colours.add(PIDColour);
382 colours.add(BLOSUM62Colour);
383 colours.add(nucleotideColour);
385 setColourSelected(jalview.bin.Cache
386 .getDefault("DEFAULT_COLOUR", "None"));
390 public void setColourSelected(String defaultColour)
393 if (defaultColour != null)
395 int index = ColourSchemeProperty
396 .getColourIndexFromName(defaultColour);
400 case ColourSchemeProperty.NONE:
401 noColourmenuItem.setSelected(true);
403 case ColourSchemeProperty.CLUSTAL:
404 clustalColour.setSelected(true);
408 case ColourSchemeProperty.BLOSUM:
409 BLOSUM62Colour.setSelected(true);
413 case ColourSchemeProperty.PID:
414 PIDColour.setSelected(true);
418 case ColourSchemeProperty.ZAPPO:
419 zappoColour.setSelected(true);
423 case ColourSchemeProperty.TAYLOR:
424 taylorColour.setSelected(true);
427 case ColourSchemeProperty.HYDROPHOBIC:
428 hydrophobicityColour.setSelected(true);
432 case ColourSchemeProperty.HELIX:
433 helixColour.setSelected(true);
437 case ColourSchemeProperty.STRAND:
438 strandColour.setSelected(true);
442 case ColourSchemeProperty.TURN:
443 turnColour.setSelected(true);
447 case ColourSchemeProperty.BURIED:
448 buriedColour.setSelected(true);
452 case ColourSchemeProperty.NUCLEOTIDE:
453 nucleotideColour.setSelected(true);
457 case ColourSchemeProperty.USER_DEFINED:
458 userDefinedColour.setSelected(true);
466 private void jbInit() throws Exception
468 fileMenu.setText("File");
469 saveAs.setText("Save As...");
470 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
471 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
472 .getMenuShortcutKeyMask()
473 | java.awt.event.KeyEvent.SHIFT_MASK, false));
474 saveAs.addActionListener(new ActionListener()
476 public void actionPerformed(ActionEvent e)
478 saveAs_actionPerformed(e);
481 closeMenuItem.setText("Close");
482 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
483 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
484 .getMenuShortcutKeyMask(), false));
485 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
487 public void actionPerformed(ActionEvent e)
489 closeMenuItem_actionPerformed(false);
492 editMenu.setText("Edit");
493 viewMenu.setText("View");
494 colourMenu.setText("Colour");
495 calculateMenu.setText("Calculate");
496 webService.setText("Web Service");
497 selectAllSequenceMenuItem.setText("Select All");
498 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
499 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
500 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
501 selectAllSequenceMenuItem
502 .addActionListener(new java.awt.event.ActionListener()
504 public void actionPerformed(ActionEvent e)
506 selectAllSequenceMenuItem_actionPerformed(e);
509 deselectAllSequenceMenuItem.setText("Deselect All");
510 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
511 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
512 deselectAllSequenceMenuItem
513 .addActionListener(new java.awt.event.ActionListener()
515 public void actionPerformed(ActionEvent e)
517 deselectAllSequenceMenuItem_actionPerformed(e);
520 invertSequenceMenuItem.setText("Invert Sequence Selection");
521 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
522 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
523 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
524 invertSequenceMenuItem
525 .addActionListener(new java.awt.event.ActionListener()
527 public void actionPerformed(ActionEvent e)
529 invertSequenceMenuItem_actionPerformed(e);
532 remove2LeftMenuItem.setText("Remove Left");
533 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
534 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
535 .getMenuShortcutKeyMask(), false));
537 .addActionListener(new java.awt.event.ActionListener()
539 public void actionPerformed(ActionEvent e)
541 remove2LeftMenuItem_actionPerformed(e);
544 remove2RightMenuItem.setText("Remove Right");
545 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
546 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
547 .getMenuShortcutKeyMask(), false));
549 .addActionListener(new java.awt.event.ActionListener()
551 public void actionPerformed(ActionEvent e)
553 remove2RightMenuItem_actionPerformed(e);
556 removeGappedColumnMenuItem.setText("Remove Empty Columns");
557 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
558 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
559 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
560 removeGappedColumnMenuItem
561 .addActionListener(new java.awt.event.ActionListener()
563 public void actionPerformed(ActionEvent e)
565 removeGappedColumnMenuItem_actionPerformed(e);
568 removeAllGapsMenuItem.setText("Remove All Gaps");
569 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
570 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
571 .getDefaultToolkit().getMenuShortcutKeyMask()
572 | java.awt.event.KeyEvent.SHIFT_MASK, false));
573 removeAllGapsMenuItem
574 .addActionListener(new java.awt.event.ActionListener()
576 public void actionPerformed(ActionEvent e)
578 removeAllGapsMenuItem_actionPerformed(e);
581 viewBoxesMenuItem.setText("Boxes");
582 viewBoxesMenuItem.setState(true);
583 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
585 public void actionPerformed(ActionEvent e)
587 viewBoxesMenuItem_actionPerformed(e);
590 viewTextMenuItem.setText("Text");
591 viewTextMenuItem.setState(true);
592 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
594 public void actionPerformed(ActionEvent e)
596 viewTextMenuItem_actionPerformed(e);
599 sortPairwiseMenuItem.setText("by Pairwise Identity");
601 .addActionListener(new java.awt.event.ActionListener()
603 public void actionPerformed(ActionEvent e)
605 sortPairwiseMenuItem_actionPerformed(e);
608 sortIDMenuItem.setText("by ID");
609 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
611 public void actionPerformed(ActionEvent e)
613 sortIDMenuItem_actionPerformed(e);
616 sortGroupMenuItem.setText("by Group");
617 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
619 public void actionPerformed(ActionEvent e)
621 sortGroupMenuItem_actionPerformed(e);
624 removeRedundancyMenuItem.setText("Remove Redundancy...");
625 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
626 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
627 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
628 removeRedundancyMenuItem
629 .addActionListener(new java.awt.event.ActionListener()
631 public void actionPerformed(ActionEvent e)
633 removeRedundancyMenuItem_actionPerformed(e);
636 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
637 pairwiseAlignmentMenuItem
638 .addActionListener(new java.awt.event.ActionListener()
640 public void actionPerformed(ActionEvent e)
642 pairwiseAlignmentMenuItem_actionPerformed(e);
645 PCAMenuItem.setText("Principal Component Analysis");
646 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
648 public void actionPerformed(ActionEvent e)
650 PCAMenuItem_actionPerformed(e);
653 averageDistanceTreeMenuItem
654 .setText("Average Distance Using % Identity");
655 averageDistanceTreeMenuItem
656 .addActionListener(new java.awt.event.ActionListener()
658 public void actionPerformed(ActionEvent e)
660 averageDistanceTreeMenuItem_actionPerformed(e);
663 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
664 neighbourTreeMenuItem
665 .addActionListener(new java.awt.event.ActionListener()
667 public void actionPerformed(ActionEvent e)
669 neighbourTreeMenuItem_actionPerformed(e);
672 this.getContentPane().setLayout(borderLayout1);
673 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
674 statusBar.setBackground(Color.white);
675 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
676 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
677 statusBar.setText("Status bar");
678 outputTextboxMenu.setText("Output to Textbox");
679 clustalColour.setText("Clustalx");
681 clustalColour.addActionListener(new java.awt.event.ActionListener()
683 public void actionPerformed(ActionEvent e)
685 clustalColour_actionPerformed(e);
688 zappoColour.setText("Zappo");
689 zappoColour.addActionListener(new java.awt.event.ActionListener()
691 public void actionPerformed(ActionEvent e)
693 zappoColour_actionPerformed(e);
696 taylorColour.setText("Taylor");
697 taylorColour.addActionListener(new java.awt.event.ActionListener()
699 public void actionPerformed(ActionEvent e)
701 taylorColour_actionPerformed(e);
704 hydrophobicityColour.setText("Hydrophobicity");
706 .addActionListener(new java.awt.event.ActionListener()
708 public void actionPerformed(ActionEvent e)
710 hydrophobicityColour_actionPerformed(e);
713 helixColour.setText("Helix Propensity");
714 helixColour.addActionListener(new java.awt.event.ActionListener()
716 public void actionPerformed(ActionEvent e)
718 helixColour_actionPerformed(e);
721 strandColour.setText("Strand Propensity");
722 strandColour.addActionListener(new java.awt.event.ActionListener()
724 public void actionPerformed(ActionEvent e)
726 strandColour_actionPerformed(e);
729 turnColour.setText("Turn Propensity");
730 turnColour.addActionListener(new java.awt.event.ActionListener()
732 public void actionPerformed(ActionEvent e)
734 turnColour_actionPerformed(e);
737 buriedColour.setText("Buried Index");
738 buriedColour.addActionListener(new java.awt.event.ActionListener()
740 public void actionPerformed(ActionEvent e)
742 buriedColour_actionPerformed(e);
745 userDefinedColour.setText("User Defined...");
746 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
748 public void actionPerformed(ActionEvent e)
750 userDefinedColour_actionPerformed(e);
753 PIDColour.setText("Percentage Identity");
754 PIDColour.addActionListener(new java.awt.event.ActionListener()
756 public void actionPerformed(ActionEvent e)
758 PIDColour_actionPerformed(e);
761 BLOSUM62Colour.setText("BLOSUM62 Score");
762 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
764 public void actionPerformed(ActionEvent e)
766 BLOSUM62Colour_actionPerformed(e);
769 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
770 avDistanceTreeBlosumMenuItem
771 .addActionListener(new java.awt.event.ActionListener()
773 public void actionPerformed(ActionEvent e)
775 avTreeBlosumMenuItem_actionPerformed(e);
778 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
780 .addActionListener(new java.awt.event.ActionListener()
782 public void actionPerformed(ActionEvent e)
784 njTreeBlosumMenuItem_actionPerformed(e);
787 annotationPanelMenuItem.setActionCommand("");
788 annotationPanelMenuItem.setText("Show Annotations");
789 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
790 "SHOW_ANNOTATIONS", true));
791 annotationPanelMenuItem
792 .addActionListener(new java.awt.event.ActionListener()
794 public void actionPerformed(ActionEvent e)
796 annotationPanelMenuItem_actionPerformed(e);
799 colourTextMenuItem.setText("Colour Text");
801 .addActionListener(new java.awt.event.ActionListener()
803 public void actionPerformed(ActionEvent e)
805 colourTextMenuItem_actionPerformed(e);
808 htmlMenuItem.setText("HTML");
809 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
811 public void actionPerformed(ActionEvent e)
813 htmlMenuItem_actionPerformed(e);
816 overviewMenuItem.setText("Overview Window");
817 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
819 public void actionPerformed(ActionEvent e)
821 overviewMenuItem_actionPerformed(e);
824 undoMenuItem.setEnabled(false);
825 undoMenuItem.setText("Undo");
826 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
827 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
828 .getMenuShortcutKeyMask(), false));
829 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
831 public void actionPerformed(ActionEvent e)
833 undoMenuItem_actionPerformed(e);
836 redoMenuItem.setEnabled(false);
837 redoMenuItem.setText("Redo");
838 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
839 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
840 .getMenuShortcutKeyMask(), false));
841 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
843 public void actionPerformed(ActionEvent e)
845 redoMenuItem_actionPerformed(e);
848 conservationMenuItem.setText("By Conservation");
850 .addActionListener(new java.awt.event.ActionListener()
852 public void actionPerformed(ActionEvent e)
854 conservationMenuItem_actionPerformed(e);
857 noColourmenuItem.setText("None");
858 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
860 public void actionPerformed(ActionEvent e)
862 noColourmenuItem_actionPerformed(e);
865 wrapMenuItem.setText("Wrap");
866 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
868 public void actionPerformed(ActionEvent e)
870 wrapMenuItem_actionPerformed(e);
873 printMenuItem.setText("Print ...");
874 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
875 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
876 .getMenuShortcutKeyMask(), false));
877 printMenuItem.addActionListener(new java.awt.event.ActionListener()
879 public void actionPerformed(ActionEvent e)
881 printMenuItem_actionPerformed(e);
884 renderGapsMenuItem.setText("Show Gaps");
885 renderGapsMenuItem.setState(true);
887 .addActionListener(new java.awt.event.ActionListener()
889 public void actionPerformed(ActionEvent e)
891 renderGapsMenuItem_actionPerformed(e);
894 findMenuItem.setText("Find...");
895 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
896 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
897 .getMenuShortcutKeyMask(), false));
898 findMenuItem.addActionListener(new java.awt.event.ActionListener()
900 public void actionPerformed(ActionEvent e)
902 findMenuItem_actionPerformed(e);
905 abovePIDThreshold.setText("Above Identity Threshold");
906 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
908 public void actionPerformed(ActionEvent e)
910 abovePIDThreshold_actionPerformed(e);
913 showSeqFeatures.setText("Show Sequence Features");
914 showSeqFeatures.addActionListener(new ActionListener()
916 public void actionPerformed(ActionEvent actionEvent)
918 showSeqFeatures_actionPerformed(actionEvent);
921 showDbRefsMenuitem.setText("Show Database Refs");
922 showDbRefsMenuitem.addActionListener(new ActionListener()
925 public void actionPerformed(ActionEvent e)
927 showDbRefs_actionPerformed(e);
931 showNpFeatsMenuitem.setText("Show Non-Positional Features");
932 showNpFeatsMenuitem.addActionListener(new ActionListener()
935 public void actionPerformed(ActionEvent e)
937 showNpFeats_actionPerformed(e);
941 nucleotideColour.setText("Nucleotide");
942 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
944 public void actionPerformed(ActionEvent e)
946 nucleotideColour_actionPerformed(e);
949 deleteGroups.setText("Undefine groups");
950 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
951 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
952 .getMenuShortcutKeyMask(), false));
953 deleteGroups.addActionListener(new java.awt.event.ActionListener()
955 public void actionPerformed(ActionEvent e)
957 deleteGroups_actionPerformed(e);
960 copy.setText("Copy");
961 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
962 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
963 .getMenuShortcutKeyMask(), false));
965 copy.addActionListener(new java.awt.event.ActionListener()
967 public void actionPerformed(ActionEvent e)
969 copy_actionPerformed(e);
973 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
974 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
975 .getMenuShortcutKeyMask(), false));
976 cut.addActionListener(new java.awt.event.ActionListener()
978 public void actionPerformed(ActionEvent e)
980 cut_actionPerformed(e);
983 delete.setText("Delete");
984 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
985 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
986 delete.addActionListener(new java.awt.event.ActionListener()
988 public void actionPerformed(ActionEvent e)
990 delete_actionPerformed(e);
993 pasteMenu.setText("Paste");
994 pasteNew.setText("To New Alignment");
995 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
996 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
997 .getMenuShortcutKeyMask()
998 | java.awt.event.KeyEvent.SHIFT_MASK, false));
999 pasteNew.addActionListener(new java.awt.event.ActionListener()
1001 public void actionPerformed(ActionEvent e)
1003 pasteNew_actionPerformed(e);
1006 pasteThis.setText("Add To This Alignment");
1007 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1008 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1009 .getMenuShortcutKeyMask(), false));
1010 pasteThis.addActionListener(new java.awt.event.ActionListener()
1012 public void actionPerformed(ActionEvent e)
1014 pasteThis_actionPerformed(e);
1017 applyToAllGroups.setText("Apply Colour To All Groups");
1018 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1020 public void actionPerformed(ActionEvent e)
1022 applyToAllGroups_actionPerformed(e);
1025 createPNG.addActionListener(new java.awt.event.ActionListener()
1027 public void actionPerformed(ActionEvent e)
1032 createPNG.setActionCommand("Save As PNG Image");
1033 createPNG.setText("PNG");
1034 font.setText("Font...");
1035 font.addActionListener(new java.awt.event.ActionListener()
1037 public void actionPerformed(ActionEvent e)
1039 font_actionPerformed(e);
1043 seqLimits.setText("Show Sequence Limits");
1044 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1045 seqLimits.addActionListener(new java.awt.event.ActionListener()
1047 public void actionPerformed(ActionEvent e)
1049 seqLimit_actionPerformed(e);
1052 epsFile.setText("EPS");
1053 epsFile.addActionListener(new java.awt.event.ActionListener()
1055 public void actionPerformed(ActionEvent e)
1060 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1061 LoadtreeMenuItem.setText("Load Associated Tree");
1062 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1064 public void actionPerformed(ActionEvent e)
1066 LoadtreeMenuItem_actionPerformed(e);
1069 scaleAbove.setVisible(false);
1070 scaleAbove.setText("Scale Above");
1071 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1073 public void actionPerformed(ActionEvent e)
1075 scaleAbove_actionPerformed(e);
1078 scaleLeft.setVisible(false);
1079 scaleLeft.setSelected(true);
1080 scaleLeft.setText("Scale Left");
1081 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1083 public void actionPerformed(ActionEvent e)
1085 scaleLeft_actionPerformed(e);
1088 scaleRight.setVisible(false);
1089 scaleRight.setSelected(true);
1090 scaleRight.setText("Scale Right");
1091 scaleRight.addActionListener(new java.awt.event.ActionListener()
1093 public void actionPerformed(ActionEvent e)
1095 scaleRight_actionPerformed(e);
1098 centreColumnLabelsMenuItem.setVisible(true);
1099 centreColumnLabelsMenuItem.setState(false);
1100 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1101 centreColumnLabelsMenuItem
1102 .addActionListener(new java.awt.event.ActionListener()
1104 public void actionPerformed(ActionEvent e)
1106 centreColumnLabels_actionPerformed(e);
1110 modifyPID.setText("Modify Identity Threshold...");
1111 modifyPID.addActionListener(new java.awt.event.ActionListener()
1113 public void actionPerformed(ActionEvent e)
1115 modifyPID_actionPerformed(e);
1118 modifyConservation.setText("Modify Conservation Threshold...");
1120 .addActionListener(new java.awt.event.ActionListener()
1122 public void actionPerformed(ActionEvent e)
1124 modifyConservation_actionPerformed(e);
1127 sortByTreeMenu.setText("By Tree Order");
1128 sort.setText("Sort");
1129 sort.addMenuListener(new MenuListener()
1131 public void menuSelected(MenuEvent e)
1136 public void menuDeselected(MenuEvent e)
1140 public void menuCanceled(MenuEvent e)
1144 sortByAnnotScore.setText("by Score");
1145 sort.add(sortByAnnotScore);
1146 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1149 public void menuCanceled(MenuEvent e)
1153 public void menuDeselected(MenuEvent e)
1157 public void menuSelected(MenuEvent e)
1159 buildSortByAnnotationScoresMenu();
1162 sortByAnnotScore.setVisible(false);
1164 calculate.setText("Calculate Tree");
1166 jMenu2.setText("Export Image");
1167 padGapsMenuitem.setText("Pad Gaps");
1168 padGapsMenuitem.setState(jalview.bin.Cache
1169 .getDefault("PAD_GAPS", false));
1170 padGapsMenuitem.addActionListener(new ActionListener()
1172 public void actionPerformed(ActionEvent e)
1174 padGapsMenuitem_actionPerformed(e);
1177 vamsasStore.setVisible(false);
1178 vamsasStore.setText("VAMSAS store");
1179 vamsasStore.addActionListener(new ActionListener()
1181 public void actionPerformed(ActionEvent e)
1183 vamsasStore_actionPerformed(e);
1186 showTranslation.setText("Translate cDNA");
1187 showTranslation.addActionListener(new ActionListener()
1189 public void actionPerformed(ActionEvent e)
1191 showTranslation_actionPerformed(e);
1194 extractScores.setText("Extract Scores...");
1195 extractScores.addActionListener(new ActionListener()
1197 public void actionPerformed(ActionEvent e)
1199 extractScores_actionPerformed(e);
1202 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1204 showProducts.setText("Get Cross References");
1206 * showProducts.addActionListener(new ActionListener() {
1208 * public void actionPerformed(ActionEvent e) {
1209 * showProducts_actionPerformed(e); } });
1211 featureSettings.setText("Feature Settings...");
1212 featureSettings.addActionListener(new ActionListener()
1214 public void actionPerformed(ActionEvent e)
1216 featureSettings_actionPerformed(e);
1219 fetchSequence.setText("Fetch Sequence(s)...");
1220 fetchSequence.addActionListener(new ActionListener()
1222 public void actionPerformed(ActionEvent e)
1224 fetchSequence_actionPerformed(e);
1228 annotationColour.setText("By Annotation...");
1229 annotationColour.addActionListener(new ActionListener()
1231 public void actionPerformed(ActionEvent e)
1233 annotationColour_actionPerformed(e);
1236 associatedData.setText("Load Features / Annotations");
1237 associatedData.addActionListener(new ActionListener()
1239 public void actionPerformed(ActionEvent e)
1241 associatedData_actionPerformed(e);
1244 autoCalculate.setText("Autocalculate Consensus");
1245 autoCalculate.setState(jalview.bin.Cache.getDefault(
1246 "AUTO_CALC_CONSENSUS", true));
1247 autoCalculate.addActionListener(new ActionListener()
1249 public void actionPerformed(ActionEvent e)
1251 autoCalculate_actionPerformed(e);
1254 addSequenceMenu.setText("Add Sequences");
1255 addFromFile.setText("From File");
1256 addFromFile.addActionListener(new ActionListener()
1258 public void actionPerformed(ActionEvent e)
1260 addFromFile_actionPerformed(e);
1263 addFromText.setText("From Textbox");
1264 addFromText.addActionListener(new ActionListener()
1266 public void actionPerformed(ActionEvent e)
1268 addFromText_actionPerformed(e);
1271 addFromURL.setText("From URL");
1272 addFromURL.addActionListener(new ActionListener()
1274 public void actionPerformed(ActionEvent e)
1276 addFromURL_actionPerformed(e);
1279 exportFeatures.setText("Export Features...");
1280 exportFeatures.addActionListener(new ActionListener()
1282 public void actionPerformed(ActionEvent e)
1284 exportFeatures_actionPerformed(e);
1287 exportAnnotations.setText("Export Annotations...");
1288 exportAnnotations.addActionListener(new ActionListener()
1290 public void actionPerformed(ActionEvent e)
1292 exportAnnotations_actionPerformed(e);
1295 statusPanel.setLayout(gridLayout1);
1296 jMenu3.setText("Show");
1297 showAllSeqs.setText("All Sequences");
1298 showAllSeqs.addActionListener(new ActionListener()
1300 public void actionPerformed(ActionEvent e)
1302 showAllSeqs_actionPerformed(e);
1305 showAllColumns.setText("All Columns");
1306 showAllColumns.addActionListener(new ActionListener()
1308 public void actionPerformed(ActionEvent e)
1310 showAllColumns_actionPerformed(e);
1313 hideMenu.setText("Hide");
1314 hideSelSequences.setText("Selected Sequences");
1315 hideSelSequences.addActionListener(new ActionListener()
1317 public void actionPerformed(ActionEvent e)
1319 hideSelSequences_actionPerformed(e);
1322 hideSelColumns.setText("Selected Columns");
1323 hideSelColumns.addActionListener(new ActionListener()
1325 public void actionPerformed(ActionEvent e)
1327 hideSelColumns_actionPerformed(e);
1330 hiddenMarkers.setText("Show Hidden Markers");
1331 hiddenMarkers.addActionListener(new ActionListener()
1333 public void actionPerformed(ActionEvent e)
1335 hiddenMarkers_actionPerformed(e);
1338 invertColSel.setText("Invert Column Selection");
1339 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1340 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1341 .getMenuShortcutKeyMask()
1342 | java.awt.event.KeyEvent.ALT_MASK, false));
1343 invertColSel.addActionListener(new ActionListener()
1345 public void actionPerformed(ActionEvent e)
1347 invertColSel_actionPerformed(e);
1350 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1352 public void stateChanged(ChangeEvent evt)
1354 JTabbedPane pane = (JTabbedPane) evt.getSource();
1355 int sel = pane.getSelectedIndex();
1356 tabSelectionChanged(sel);
1359 tabbedPane.addMouseListener(new MouseAdapter()
1361 public void mousePressed(MouseEvent e)
1363 tabbedPane_mousePressed(e);
1366 tabbedPane.addFocusListener(new FocusAdapter()
1368 public void focusGained(FocusEvent e)
1370 tabbedPane_focusGained(e);
1373 save.setText("Save");
1374 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1375 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1376 .getMenuShortcutKeyMask(), false));
1377 save.addActionListener(new ActionListener()
1379 public void actionPerformed(ActionEvent e)
1381 save_actionPerformed(e);
1384 reload.setEnabled(false);
1385 reload.setText("Reload");
1386 reload.addActionListener(new ActionListener()
1388 public void actionPerformed(ActionEvent e)
1390 reload_actionPerformed(e);
1393 newView.setText("New View");
1394 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1395 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1396 .getMenuShortcutKeyMask(), false));
1397 newView.addActionListener(new ActionListener()
1399 public void actionPerformed(ActionEvent e)
1401 newView_actionPerformed(e);
1404 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1405 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1406 textColour.setText("Colour Text ...");
1407 textColour.addActionListener(new ActionListener()
1409 public void actionPerformed(ActionEvent e)
1411 textColour_actionPerformed(e);
1414 formatMenu.setText("Format");
1415 selectMenu.setText("Select");
1416 idRightAlign.setText("Right Align Sequence Id");
1417 idRightAlign.addActionListener(new ActionListener()
1419 public void actionPerformed(ActionEvent e)
1421 idRightAlign_actionPerformed(e);
1424 gatherViews.setEnabled(false);
1425 gatherViews.setText("Gather Views");
1426 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1427 java.awt.event.KeyEvent.VK_G, 0, false));
1428 gatherViews.addActionListener(new ActionListener()
1430 public void actionPerformed(ActionEvent e)
1432 gatherViews_actionPerformed(e);
1435 expandViews.setEnabled(false);
1436 expandViews.setText("Expand Views");
1437 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1438 java.awt.event.KeyEvent.VK_X, 0, false));
1439 expandViews.addActionListener(new ActionListener()
1441 public void actionPerformed(ActionEvent e)
1443 expandViews_actionPerformed(e);
1446 pageSetup.setText("Page Setup ...");
1447 pageSetup.addActionListener(new ActionListener()
1449 public void actionPerformed(ActionEvent e)
1451 pageSetup_actionPerformed(e);
1454 alignmentProperties.setText("Alignment Properties...");
1455 alignmentProperties.addActionListener(new ActionListener()
1457 public void actionPerformed(ActionEvent actionEvent)
1459 alignmentProperties();
1462 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1463 alignFrameMenuBar.add(fileMenu);
1464 alignFrameMenuBar.add(editMenu);
1465 alignFrameMenuBar.add(selectMenu);
1466 alignFrameMenuBar.add(viewMenu);
1467 alignFrameMenuBar.add(formatMenu);
1468 alignFrameMenuBar.add(colourMenu);
1469 alignFrameMenuBar.add(calculateMenu);
1470 alignFrameMenuBar.add(webService);
1471 fileMenu.add(fetchSequence);
1472 fileMenu.add(addSequenceMenu);
1473 fileMenu.add(reload);
1474 fileMenu.addSeparator();
1475 fileMenu.add(vamsasStore);
1477 fileMenu.add(saveAs);
1478 fileMenu.add(outputTextboxMenu);
1479 fileMenu.add(pageSetup);
1480 fileMenu.add(printMenuItem);
1481 fileMenu.addSeparator();
1482 fileMenu.add(jMenu2);
1483 fileMenu.add(exportFeatures);
1484 fileMenu.add(exportAnnotations);
1485 fileMenu.add(LoadtreeMenuItem);
1486 fileMenu.add(associatedData);
1487 fileMenu.addSeparator();
1488 fileMenu.add(closeMenuItem);
1489 editMenu.add(undoMenuItem);
1490 editMenu.add(redoMenuItem);
1493 editMenu.add(pasteMenu);
1494 editMenu.add(delete);
1495 editMenu.addSeparator();
1496 editMenu.add(remove2LeftMenuItem);
1497 editMenu.add(remove2RightMenuItem);
1498 editMenu.add(removeGappedColumnMenuItem);
1499 editMenu.add(removeAllGapsMenuItem);
1500 editMenu.add(removeRedundancyMenuItem);
1501 editMenu.addSeparator();
1502 editMenu.add(padGapsMenuitem);
1503 viewMenu.add(newView);
1504 viewMenu.add(expandViews);
1505 viewMenu.add(gatherViews);
1506 viewMenu.addSeparator();
1507 viewMenu.add(jMenu3);
1508 viewMenu.add(hideMenu);
1509 viewMenu.addSeparator();
1510 viewMenu.add(annotationPanelMenuItem);
1511 viewMenu.addSeparator();
1512 viewMenu.add(showSeqFeatures);
1513 viewMenu.add(featureSettings);
1514 tooltipSettingsMenu.add(showDbRefsMenuitem);
1515 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1516 viewMenu.add(tooltipSettingsMenu);
1517 viewMenu.addSeparator();
1518 viewMenu.add(alignmentProperties);
1519 viewMenu.addSeparator();
1520 viewMenu.add(overviewMenuItem);
1521 colourMenu.add(applyToAllGroups);
1522 colourMenu.add(textColour);
1523 colourMenu.addSeparator();
1524 colourMenu.add(noColourmenuItem);
1525 colourMenu.add(clustalColour);
1526 colourMenu.add(BLOSUM62Colour);
1527 colourMenu.add(PIDColour);
1528 colourMenu.add(zappoColour);
1529 colourMenu.add(taylorColour);
1530 colourMenu.add(hydrophobicityColour);
1531 colourMenu.add(helixColour);
1532 colourMenu.add(strandColour);
1533 colourMenu.add(turnColour);
1534 colourMenu.add(buriedColour);
1535 colourMenu.add(nucleotideColour);
1536 colourMenu.add(userDefinedColour);
1537 colourMenu.addSeparator();
1538 colourMenu.add(conservationMenuItem);
1539 colourMenu.add(modifyConservation);
1540 colourMenu.add(abovePIDThreshold);
1541 colourMenu.add(modifyPID);
1542 colourMenu.add(annotationColour);
1543 calculateMenu.add(sort);
1544 calculateMenu.add(calculate);
1545 calculateMenu.addSeparator();
1546 calculateMenu.add(pairwiseAlignmentMenuItem);
1547 calculateMenu.add(PCAMenuItem);
1548 calculateMenu.addSeparator();
1549 calculateMenu.add(showTranslation);
1550 calculateMenu.add(showProducts);
1551 calculateMenu.add(autoCalculate);
1552 calculateMenu.addSeparator();
1553 calculateMenu.add(extractScores);
1554 webServiceNoServices = new JMenuItem("<No Services>");
1555 webService.add(webServiceNoServices);
1556 pasteMenu.add(pasteNew);
1557 pasteMenu.add(pasteThis);
1558 sort.add(sortIDMenuItem);
1559 sort.add(sortGroupMenuItem);
1560 sort.add(sortPairwiseMenuItem);
1561 sort.add(sortByTreeMenu);
1562 calculate.add(averageDistanceTreeMenuItem);
1563 calculate.add(neighbourTreeMenuItem);
1564 calculate.add(avDistanceTreeBlosumMenuItem);
1565 calculate.add(njTreeBlosumMenuItem);
1566 jMenu2.add(htmlMenuItem);
1567 jMenu2.add(epsFile);
1568 jMenu2.add(createPNG);
1569 addSequenceMenu.add(addFromFile);
1570 addSequenceMenu.add(addFromText);
1571 addSequenceMenu.add(addFromURL);
1572 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1573 statusPanel.add(statusBar, null);
1574 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1575 jMenu3.add(showAllColumns);
1576 jMenu3.add(showAllSeqs);
1577 hideMenu.add(hideSelColumns);
1578 hideMenu.add(hideSelSequences);
1579 formatMenu.add(font);
1580 formatMenu.addSeparator();
1581 formatMenu.add(wrapMenuItem);
1582 formatMenu.add(scaleAbove);
1583 formatMenu.add(scaleLeft);
1584 formatMenu.add(scaleRight);
1585 formatMenu.add(seqLimits);
1586 formatMenu.add(idRightAlign);
1587 formatMenu.add(hiddenMarkers);
1588 formatMenu.add(viewBoxesMenuItem);
1589 formatMenu.add(viewTextMenuItem);
1590 formatMenu.add(colourTextMenuItem);
1591 formatMenu.add(renderGapsMenuItem);
1592 formatMenu.add(centreColumnLabelsMenuItem);
1593 selectMenu.add(findMenuItem);
1594 selectMenu.addSeparator();
1595 selectMenu.add(selectAllSequenceMenuItem);
1596 selectMenu.add(deselectAllSequenceMenuItem);
1597 selectMenu.add(invertSequenceMenuItem);
1598 selectMenu.add(invertColSel);
1599 selectMenu.add(deleteGroups);
1602 protected void showNpFeats_actionPerformed(ActionEvent e)
1604 // TODO Auto-generated method stub
1608 protected void showDbRefs_actionPerformed(ActionEvent e)
1610 // TODO Auto-generated method stub
1614 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1618 protected void showProducts_actionPerformed(ActionEvent e)
1622 protected void buildSortByAnnotationScoresMenu()
1626 protected void extractScores_actionPerformed(ActionEvent e)
1630 protected void outputText_actionPerformed(ActionEvent e)
1634 public void addFromFile_actionPerformed(ActionEvent e)
1639 public void addFromText_actionPerformed(ActionEvent e)
1644 public void addFromURL_actionPerformed(ActionEvent e)
1649 public void exportFeatures_actionPerformed(ActionEvent e)
1654 public void exportAnnotations_actionPerformed(ActionEvent e)
1659 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1663 protected void closeMenuItem_actionPerformed(boolean b)
1667 protected void redoMenuItem_actionPerformed(ActionEvent e)
1671 protected void undoMenuItem_actionPerformed(ActionEvent e)
1675 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1679 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1683 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1687 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1691 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1695 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1699 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1703 protected void wrapMenuItem_actionPerformed(ActionEvent e)
1707 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1711 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1715 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1719 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1723 protected void overviewMenuItem_actionPerformed(ActionEvent e)
1727 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1731 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1735 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1739 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1743 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1747 protected void PCAMenuItem_actionPerformed(ActionEvent e)
1751 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1755 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1759 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1763 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1767 protected void clustalColour_actionPerformed(ActionEvent e)
1771 protected void zappoColour_actionPerformed(ActionEvent e)
1775 protected void taylorColour_actionPerformed(ActionEvent e)
1779 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1783 protected void helixColour_actionPerformed(ActionEvent e)
1787 protected void strandColour_actionPerformed(ActionEvent e)
1791 protected void turnColour_actionPerformed(ActionEvent e)
1795 protected void buriedColour_actionPerformed(ActionEvent e)
1799 protected void userDefinedColour_actionPerformed(ActionEvent e)
1803 protected void PIDColour_actionPerformed(ActionEvent e)
1807 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1811 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1815 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1819 protected void printMenuItem_actionPerformed(ActionEvent e)
1823 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1827 protected void findMenuItem_actionPerformed(ActionEvent e)
1831 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1835 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
1839 protected void nucleotideColour_actionPerformed(ActionEvent e)
1843 protected void deleteGroups_actionPerformed(ActionEvent e)
1847 protected void copy_actionPerformed(ActionEvent e)
1851 protected void cut_actionPerformed(ActionEvent e)
1855 protected void delete_actionPerformed(ActionEvent e)
1859 protected void pasteNew_actionPerformed(ActionEvent e)
1863 protected void pasteThis_actionPerformed(ActionEvent e)
1867 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1871 public void createPNG(java.io.File f)
1875 protected void font_actionPerformed(ActionEvent e)
1879 protected void seqLimit_actionPerformed(ActionEvent e)
1883 public void seqDBRef_actionPerformed(ActionEvent e)
1888 public void createEPS(java.io.File f)
1892 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
1896 protected void jpred_actionPerformed(ActionEvent e)
1900 protected void scaleAbove_actionPerformed(ActionEvent e)
1904 protected void scaleLeft_actionPerformed(ActionEvent e)
1908 protected void scaleRight_actionPerformed(ActionEvent e)
1912 protected void modifyPID_actionPerformed(ActionEvent e)
1916 protected void modifyConservation_actionPerformed(ActionEvent e)
1920 protected void saveAs_actionPerformed(ActionEvent e)
1924 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
1928 public void vamsasStore_actionPerformed(ActionEvent e)
1933 public void vamsasLoad_actionPerformed(ActionEvent e)
1938 public void showTranslation_actionPerformed(ActionEvent e)
1943 public void featureSettings_actionPerformed(ActionEvent e)
1948 public void fetchSequence_actionPerformed(ActionEvent e)
1953 public void smoothFont_actionPerformed(ActionEvent e)
1958 public void annotationColour_actionPerformed(ActionEvent e)
1963 public void associatedData_actionPerformed(ActionEvent e)
1968 public void autoCalculate_actionPerformed(ActionEvent e)
1973 public void showAllSeqs_actionPerformed(ActionEvent e)
1978 public void showAllColumns_actionPerformed(ActionEvent e)
1983 public void hideSelSequences_actionPerformed(ActionEvent e)
1988 public void hideSelColumns_actionPerformed(ActionEvent e)
1993 public void hiddenMarkers_actionPerformed(ActionEvent e)
1998 public void findPdbId_actionPerformed(ActionEvent e)
2003 public void enterPdbId_actionPerformed(ActionEvent e)
2008 public void pdbFile_actionPerformed(ActionEvent e)
2013 public void invertColSel_actionPerformed(ActionEvent e)
2018 public void tabSelectionChanged(int sel)
2023 public void tabbedPane_mousePressed(MouseEvent e)
2028 public void tabbedPane_focusGained(FocusEvent e)
2033 public void save_actionPerformed(ActionEvent e)
2038 public void reload_actionPerformed(ActionEvent e)
2043 public void newView_actionPerformed(ActionEvent e)
2048 public void textColour_actionPerformed(ActionEvent e)
2053 public void idRightAlign_actionPerformed(ActionEvent e)
2058 public void expandViews_actionPerformed(ActionEvent e)
2063 public void gatherViews_actionPerformed(ActionEvent e)
2068 public void buildTreeMenu()
2073 public void pageSetup_actionPerformed(ActionEvent e)
2078 public void alignmentProperties()