2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 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 sortLengthMenuItem = new JMenuItem();
73 protected JMenuItem sortGroupMenuItem = new JMenuItem();
75 protected JMenu sortByAnnotScore = new JMenu();
77 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
79 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
81 protected JMenuItem PCAMenuItem = new JMenuItem();
83 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
85 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
87 BorderLayout borderLayout1 = new BorderLayout();
89 public JLabel statusBar = new JLabel();
91 protected JMenuItem saveAs = new JMenuItem();
93 protected JMenu outputTextboxMenu = new JMenu();
95 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
97 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
99 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
101 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
103 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
105 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
107 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
109 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
111 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
113 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
115 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
117 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
119 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
121 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
123 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
125 public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
127 JMenuItem htmlMenuItem = new JMenuItem();
129 JMenuItem overviewMenuItem = new JMenuItem();
131 protected JMenuItem undoMenuItem = new JMenuItem();
133 protected JMenuItem redoMenuItem = new JMenuItem();
135 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
137 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
139 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
141 JMenuItem printMenuItem = new JMenuItem();
143 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
145 JMenuItem findMenuItem = new JMenuItem();
147 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
149 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
150 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
152 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
154 JMenuItem deleteGroups = new JMenuItem();
156 JMenuItem delete = new JMenuItem();
158 JMenuItem copy = new JMenuItem();
160 JMenuItem cut = new JMenuItem();
162 JMenu pasteMenu = new JMenu();
164 JMenuItem pasteNew = new JMenuItem();
166 JMenuItem pasteThis = new JMenuItem();
168 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
170 JMenuItem createPNG = new JMenuItem();
172 protected JMenuItem font = new JMenuItem();
174 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
176 JMenuItem epsFile = new JMenuItem();
178 JMenuItem LoadtreeMenuItem = new JMenuItem();
180 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
182 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
184 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
186 protected JMenuItem modifyPID = new JMenuItem();
188 protected JMenuItem modifyConservation = new JMenuItem();
190 protected JMenu sortByTreeMenu = new JMenu();
192 protected JMenu sort = new JMenu();
194 protected JMenu calculateTree = new JMenu();
196 JMenu jMenu2 = new JMenu();
198 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
199 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
200 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
202 protected ButtonGroup colours = new ButtonGroup();
204 JMenuItem vamsasStore = new JMenuItem();
206 protected JMenuItem showTranslation = new JMenuItem();
208 protected JMenuItem extractScores = new JMenuItem();
210 protected JMenu showProducts = new JMenu();
212 public JMenuItem featureSettings = new JMenuItem();
214 JMenuItem fetchSequence = new JMenuItem();
216 JMenuItem annotationColour = new JMenuItem();
218 JMenuItem associatedData = new JMenuItem();
220 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
222 JMenu addSequenceMenu = new JMenu();
224 JMenuItem addFromFile = new JMenuItem();
226 JMenuItem addFromText = new JMenuItem();
228 JMenuItem addFromURL = new JMenuItem();
230 JMenuItem exportAnnotations = new JMenuItem();
232 JMenuItem exportFeatures = new JMenuItem();
234 protected JPanel statusPanel = new JPanel();
236 GridLayout gridLayout1 = new GridLayout();
238 JMenu jMenu3 = new JMenu();
240 JMenuItem showAllSeqs = new JMenuItem();
242 JMenuItem showAllColumns = new JMenuItem();
244 JMenu hideMenu = new JMenu();
246 JMenuItem hideSelSequences = new JMenuItem();
248 JMenuItem hideSelColumns = new JMenuItem();
250 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
252 JMenuItem invertColSel = new JMenuItem();
254 protected JTabbedPane tabbedPane = new JTabbedPane();
256 JMenuItem save = new JMenuItem();
258 protected JMenuItem reload = new JMenuItem();
260 JMenuItem newView = new JMenuItem();
262 JMenuItem textColour = new JMenuItem();
264 JMenu formatMenu = new JMenu();
266 JMenu selectMenu = new JMenu();
268 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
270 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
272 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
274 protected JMenuItem gatherViews = new JMenuItem();
276 protected JMenuItem expandViews = new JMenuItem();
278 JMenuItem pageSetup = new JMenuItem();
280 JMenuItem alignmentProperties = new JMenuItem();
282 JMenu tooltipSettingsMenu = new JMenu();
284 private JMenuItem justifyLeftMenuItem=new JMenuItem();
286 private JMenuItem justifyRightMenuItem=new JMenuItem();
288 protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
289 protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
291 private JMenuItem grpsFromSelection = new JMenuItem();
297 setJMenuBar(alignFrameMenuBar);
299 // dynamically fill save as menu with available formats
300 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
302 JMenuItem item = new JMenuItem(
303 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
305 item.addActionListener(new java.awt.event.ActionListener()
307 public void actionPerformed(ActionEvent e)
309 outputText_actionPerformed(e);
313 outputTextboxMenu.add(item);
315 } catch (Exception e)
319 if (!new jalview.util.Platform().isAMac())
321 closeMenuItem.setMnemonic('C');
322 outputTextboxMenu.setMnemonic('T');
323 undoMenuItem.setMnemonic('Z');
324 redoMenuItem.setMnemonic('0');
325 copy.setMnemonic('C');
326 cut.setMnemonic('U');
327 pasteMenu.setMnemonic('P');
328 reload.setMnemonic('R');
331 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
333 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
334 .getUserColourSchemes().keys();
336 while (userColours.hasMoreElements())
338 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
339 userColours.nextElement().toString());
340 radioItem.setName("USER_DEFINED");
341 radioItem.addMouseListener(new MouseAdapter()
343 public void mousePressed(MouseEvent evt)
345 if (evt.isControlDown()
346 || SwingUtilities.isRightMouseButton(evt))
349 .removeActionListener(radioItem.getActionListeners()[0]);
351 int option = JOptionPane.showInternalConfirmDialog(
352 jalview.gui.Desktop.desktop,
353 "Remove from default list?",
354 "Remove user defined colour",
355 JOptionPane.YES_NO_OPTION);
356 if (option == JOptionPane.YES_OPTION)
358 jalview.gui.UserDefinedColours
359 .removeColourFromDefaults(radioItem.getText());
360 colourMenu.remove(radioItem);
364 radioItem.addActionListener(new ActionListener()
366 public void actionPerformed(ActionEvent evt)
368 userDefinedColour_actionPerformed(evt);
375 radioItem.addActionListener(new ActionListener()
377 public void actionPerformed(ActionEvent evt)
379 userDefinedColour_actionPerformed(evt);
382 colourMenu.insert(radioItem, 15);
383 colours.add(radioItem);
386 colours.add(noColourmenuItem);
387 colours.add(clustalColour);
388 colours.add(zappoColour);
389 colours.add(taylorColour);
390 colours.add(hydrophobicityColour);
391 colours.add(helixColour);
392 colours.add(strandColour);
393 colours.add(turnColour);
394 colours.add(buriedColour);
395 colours.add(userDefinedColour);
396 colours.add(PIDColour);
397 colours.add(BLOSUM62Colour);
398 colours.add(nucleotideColour);
400 setColourSelected(jalview.bin.Cache
401 .getDefault("DEFAULT_COLOUR", "None"));
405 public void setColourSelected(String defaultColour)
408 if (defaultColour != null)
410 int index = ColourSchemeProperty
411 .getColourIndexFromName(defaultColour);
415 case ColourSchemeProperty.NONE:
416 noColourmenuItem.setSelected(true);
418 case ColourSchemeProperty.CLUSTAL:
419 clustalColour.setSelected(true);
423 case ColourSchemeProperty.BLOSUM:
424 BLOSUM62Colour.setSelected(true);
428 case ColourSchemeProperty.PID:
429 PIDColour.setSelected(true);
433 case ColourSchemeProperty.ZAPPO:
434 zappoColour.setSelected(true);
438 case ColourSchemeProperty.TAYLOR:
439 taylorColour.setSelected(true);
442 case ColourSchemeProperty.HYDROPHOBIC:
443 hydrophobicityColour.setSelected(true);
447 case ColourSchemeProperty.HELIX:
448 helixColour.setSelected(true);
452 case ColourSchemeProperty.STRAND:
453 strandColour.setSelected(true);
457 case ColourSchemeProperty.TURN:
458 turnColour.setSelected(true);
462 case ColourSchemeProperty.BURIED:
463 buriedColour.setSelected(true);
467 case ColourSchemeProperty.NUCLEOTIDE:
468 nucleotideColour.setSelected(true);
472 case ColourSchemeProperty.USER_DEFINED:
473 userDefinedColour.setSelected(true);
481 private void jbInit() throws Exception
483 fileMenu.setText("File");
484 saveAs.setText("Save As...");
485 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
486 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
487 .getMenuShortcutKeyMask()
488 | java.awt.event.KeyEvent.SHIFT_MASK, false));
489 saveAs.addActionListener(new ActionListener()
491 public void actionPerformed(ActionEvent e)
493 saveAs_actionPerformed(e);
496 closeMenuItem.setText("Close");
497 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
498 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
499 .getMenuShortcutKeyMask(), false));
500 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
502 public void actionPerformed(ActionEvent e)
504 closeMenuItem_actionPerformed(false);
507 editMenu.setText("Edit");
508 viewMenu.setText("View");
509 colourMenu.setText("Colour");
510 calculateMenu.setText("Calculate");
511 webService.setText("Web Service");
512 selectAllSequenceMenuItem.setText("Select All");
513 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
514 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
515 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
516 selectAllSequenceMenuItem
517 .addActionListener(new java.awt.event.ActionListener()
519 public void actionPerformed(ActionEvent e)
521 selectAllSequenceMenuItem_actionPerformed(e);
524 deselectAllSequenceMenuItem.setText("Deselect All");
525 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
526 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
527 deselectAllSequenceMenuItem
528 .addActionListener(new java.awt.event.ActionListener()
530 public void actionPerformed(ActionEvent e)
532 deselectAllSequenceMenuItem_actionPerformed(e);
535 invertSequenceMenuItem.setText("Invert Sequence Selection");
536 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
537 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
538 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
539 invertSequenceMenuItem
540 .addActionListener(new java.awt.event.ActionListener()
542 public void actionPerformed(ActionEvent e)
544 invertSequenceMenuItem_actionPerformed(e);
547 grpsFromSelection.setText("Make Groups for selection");
548 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
550 public void actionPerformed(ActionEvent e)
552 makeGrpsFromSelection_actionPerformed(e);
556 remove2LeftMenuItem.setText("Remove Left");
557 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
558 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
559 .getMenuShortcutKeyMask(), false));
561 .addActionListener(new java.awt.event.ActionListener()
563 public void actionPerformed(ActionEvent e)
565 remove2LeftMenuItem_actionPerformed(e);
568 remove2RightMenuItem.setText("Remove Right");
569 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
570 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
571 .getMenuShortcutKeyMask(), false));
573 .addActionListener(new java.awt.event.ActionListener()
575 public void actionPerformed(ActionEvent e)
577 remove2RightMenuItem_actionPerformed(e);
580 removeGappedColumnMenuItem.setText("Remove Empty Columns");
581 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
582 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
583 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
584 removeGappedColumnMenuItem
585 .addActionListener(new java.awt.event.ActionListener()
587 public void actionPerformed(ActionEvent e)
589 removeGappedColumnMenuItem_actionPerformed(e);
592 removeAllGapsMenuItem.setText("Remove All Gaps");
593 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
594 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
595 .getDefaultToolkit().getMenuShortcutKeyMask()
596 | java.awt.event.KeyEvent.SHIFT_MASK, false));
597 removeAllGapsMenuItem
598 .addActionListener(new java.awt.event.ActionListener()
600 public void actionPerformed(ActionEvent e)
602 removeAllGapsMenuItem_actionPerformed(e);
605 justifyLeftMenuItem.setText("Left Justify Alignment");
606 justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
608 public void actionPerformed(ActionEvent e)
610 justifyLeftMenuItem_actionPerformed(e);
613 justifyRightMenuItem.setText("Right Justify Alignment");
614 justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
616 public void actionPerformed(ActionEvent e)
618 justifyRightMenuItem_actionPerformed(e);
621 viewBoxesMenuItem.setText("Boxes");
622 viewBoxesMenuItem.setState(true);
623 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
625 public void actionPerformed(ActionEvent e)
627 viewBoxesMenuItem_actionPerformed(e);
630 viewTextMenuItem.setText("Text");
631 viewTextMenuItem.setState(true);
632 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
634 public void actionPerformed(ActionEvent e)
636 viewTextMenuItem_actionPerformed(e);
639 showUnconservedMenuItem.setText("Show Unconserved");
640 showUnconservedMenuItem.setState(false);
641 showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
643 public void actionPerformed(ActionEvent e)
645 showUnconservedMenuItem_actionPerformed(e);
648 sortPairwiseMenuItem.setText("by Pairwise Identity");
650 .addActionListener(new java.awt.event.ActionListener()
652 public void actionPerformed(ActionEvent e)
654 sortPairwiseMenuItem_actionPerformed(e);
657 sortIDMenuItem.setText("by ID");
658 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
660 public void actionPerformed(ActionEvent e)
662 sortIDMenuItem_actionPerformed(e);
665 sortLengthMenuItem.setText("By Length");
666 sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
668 public void actionPerformed(ActionEvent e)
670 sortLengthMenuItem_actionPerformed(e);
673 sortGroupMenuItem.setText("by Group");
674 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
676 public void actionPerformed(ActionEvent e)
678 sortGroupMenuItem_actionPerformed(e);
681 removeRedundancyMenuItem.setText("Remove Redundancy...");
682 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
683 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
684 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
685 removeRedundancyMenuItem
686 .addActionListener(new java.awt.event.ActionListener()
688 public void actionPerformed(ActionEvent e)
690 removeRedundancyMenuItem_actionPerformed(e);
693 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
694 pairwiseAlignmentMenuItem
695 .addActionListener(new java.awt.event.ActionListener()
697 public void actionPerformed(ActionEvent e)
699 pairwiseAlignmentMenuItem_actionPerformed(e);
702 PCAMenuItem.setText("Principal Component Analysis");
703 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
705 public void actionPerformed(ActionEvent e)
707 PCAMenuItem_actionPerformed(e);
710 averageDistanceTreeMenuItem
711 .setText("Average Distance Using % Identity");
712 averageDistanceTreeMenuItem
713 .addActionListener(new java.awt.event.ActionListener()
715 public void actionPerformed(ActionEvent e)
717 averageDistanceTreeMenuItem_actionPerformed(e);
720 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
721 neighbourTreeMenuItem
722 .addActionListener(new java.awt.event.ActionListener()
724 public void actionPerformed(ActionEvent e)
726 neighbourTreeMenuItem_actionPerformed(e);
729 this.getContentPane().setLayout(borderLayout1);
730 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
731 statusBar.setBackground(Color.white);
732 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
733 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
734 statusBar.setText("Status bar");
735 outputTextboxMenu.setText("Output to Textbox");
736 clustalColour.setText("Clustalx");
738 clustalColour.addActionListener(new java.awt.event.ActionListener()
740 public void actionPerformed(ActionEvent e)
742 clustalColour_actionPerformed(e);
745 zappoColour.setText("Zappo");
746 zappoColour.addActionListener(new java.awt.event.ActionListener()
748 public void actionPerformed(ActionEvent e)
750 zappoColour_actionPerformed(e);
753 taylorColour.setText("Taylor");
754 taylorColour.addActionListener(new java.awt.event.ActionListener()
756 public void actionPerformed(ActionEvent e)
758 taylorColour_actionPerformed(e);
761 hydrophobicityColour.setText("Hydrophobicity");
763 .addActionListener(new java.awt.event.ActionListener()
765 public void actionPerformed(ActionEvent e)
767 hydrophobicityColour_actionPerformed(e);
770 helixColour.setText("Helix Propensity");
771 helixColour.addActionListener(new java.awt.event.ActionListener()
773 public void actionPerformed(ActionEvent e)
775 helixColour_actionPerformed(e);
778 strandColour.setText("Strand Propensity");
779 strandColour.addActionListener(new java.awt.event.ActionListener()
781 public void actionPerformed(ActionEvent e)
783 strandColour_actionPerformed(e);
786 turnColour.setText("Turn Propensity");
787 turnColour.addActionListener(new java.awt.event.ActionListener()
789 public void actionPerformed(ActionEvent e)
791 turnColour_actionPerformed(e);
794 buriedColour.setText("Buried Index");
795 buriedColour.addActionListener(new java.awt.event.ActionListener()
797 public void actionPerformed(ActionEvent e)
799 buriedColour_actionPerformed(e);
802 userDefinedColour.setText("User Defined...");
803 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
805 public void actionPerformed(ActionEvent e)
807 userDefinedColour_actionPerformed(e);
810 PIDColour.setText("Percentage Identity");
811 PIDColour.addActionListener(new java.awt.event.ActionListener()
813 public void actionPerformed(ActionEvent e)
815 PIDColour_actionPerformed(e);
818 BLOSUM62Colour.setText("BLOSUM62 Score");
819 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
821 public void actionPerformed(ActionEvent e)
823 BLOSUM62Colour_actionPerformed(e);
826 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
827 avDistanceTreeBlosumMenuItem
828 .addActionListener(new java.awt.event.ActionListener()
830 public void actionPerformed(ActionEvent e)
832 avTreeBlosumMenuItem_actionPerformed(e);
835 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
837 .addActionListener(new java.awt.event.ActionListener()
839 public void actionPerformed(ActionEvent e)
841 njTreeBlosumMenuItem_actionPerformed(e);
844 annotationPanelMenuItem.setActionCommand("");
845 annotationPanelMenuItem.setText("Show Annotations");
846 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
847 "SHOW_ANNOTATIONS", true));
848 annotationPanelMenuItem
849 .addActionListener(new java.awt.event.ActionListener()
851 public void actionPerformed(ActionEvent e)
853 annotationPanelMenuItem_actionPerformed(e);
856 colourTextMenuItem.setText("Colour Text");
858 .addActionListener(new java.awt.event.ActionListener()
860 public void actionPerformed(ActionEvent e)
862 colourTextMenuItem_actionPerformed(e);
865 htmlMenuItem.setText("HTML");
866 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
868 public void actionPerformed(ActionEvent e)
870 htmlMenuItem_actionPerformed(e);
873 overviewMenuItem.setText("Overview Window");
874 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
876 public void actionPerformed(ActionEvent e)
878 overviewMenuItem_actionPerformed(e);
881 undoMenuItem.setEnabled(false);
882 undoMenuItem.setText("Undo");
883 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
884 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
885 .getMenuShortcutKeyMask(), false));
886 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
888 public void actionPerformed(ActionEvent e)
890 undoMenuItem_actionPerformed(e);
893 redoMenuItem.setEnabled(false);
894 redoMenuItem.setText("Redo");
895 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
896 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
897 .getMenuShortcutKeyMask(), false));
898 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
900 public void actionPerformed(ActionEvent e)
902 redoMenuItem_actionPerformed(e);
905 conservationMenuItem.setText("By Conservation");
907 .addActionListener(new java.awt.event.ActionListener()
909 public void actionPerformed(ActionEvent e)
911 conservationMenuItem_actionPerformed(e);
914 noColourmenuItem.setText("None");
915 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
917 public void actionPerformed(ActionEvent e)
919 noColourmenuItem_actionPerformed(e);
922 wrapMenuItem.setText("Wrap");
923 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
925 public void actionPerformed(ActionEvent e)
927 wrapMenuItem_actionPerformed(e);
930 printMenuItem.setText("Print ...");
931 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
932 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
933 .getMenuShortcutKeyMask(), false));
934 printMenuItem.addActionListener(new java.awt.event.ActionListener()
936 public void actionPerformed(ActionEvent e)
938 printMenuItem_actionPerformed(e);
941 renderGapsMenuItem.setText("Show Gaps");
942 renderGapsMenuItem.setState(true);
944 .addActionListener(new java.awt.event.ActionListener()
946 public void actionPerformed(ActionEvent e)
948 renderGapsMenuItem_actionPerformed(e);
951 findMenuItem.setText("Find...");
952 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
953 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
954 .getMenuShortcutKeyMask(), false));
955 findMenuItem.addActionListener(new java.awt.event.ActionListener()
957 public void actionPerformed(ActionEvent e)
959 findMenuItem_actionPerformed(e);
962 abovePIDThreshold.setText("Above Identity Threshold");
963 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
965 public void actionPerformed(ActionEvent e)
967 abovePIDThreshold_actionPerformed(e);
970 showSeqFeatures.setText("Show Sequence Features");
971 showSeqFeatures.addActionListener(new ActionListener()
973 public void actionPerformed(ActionEvent actionEvent)
975 showSeqFeatures_actionPerformed(actionEvent);
978 showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
979 showSeqFeaturesHeight.addActionListener(new ActionListener()
981 public void actionPerformed(ActionEvent actionEvent)
983 showSeqFeaturesHeight_actionPerformed(actionEvent);
986 showDbRefsMenuitem.setText("Show Database Refs");
987 showDbRefsMenuitem.addActionListener(new ActionListener()
990 public void actionPerformed(ActionEvent e)
992 showDbRefs_actionPerformed(e);
996 showNpFeatsMenuitem.setText("Show Non-Positional Features");
997 showNpFeatsMenuitem.addActionListener(new ActionListener()
1000 public void actionPerformed(ActionEvent e)
1002 showNpFeats_actionPerformed(e);
1006 showGroupConservation.setText("Group Conservation");
1007 showGroupConservation.addActionListener(new ActionListener()
1010 public void actionPerformed(ActionEvent e)
1012 showGroupConservation_actionPerformed(e);
1017 showGroupConsensus.setText("Group Consensus");
1018 showGroupConsensus.addActionListener(new ActionListener()
1021 public void actionPerformed(ActionEvent e)
1023 showGroupConsensus_actionPerformed(e);
1028 nucleotideColour.setText("Nucleotide");
1029 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1031 public void actionPerformed(ActionEvent e)
1033 nucleotideColour_actionPerformed(e);
1036 deleteGroups.setText("Undefine groups");
1037 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1038 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1039 .getMenuShortcutKeyMask(), false));
1040 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 deleteGroups_actionPerformed(e);
1047 copy.setText("Copy");
1048 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1049 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1050 .getMenuShortcutKeyMask(), false));
1052 copy.addActionListener(new java.awt.event.ActionListener()
1054 public void actionPerformed(ActionEvent e)
1056 copy_actionPerformed(e);
1060 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1061 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1062 .getMenuShortcutKeyMask(), false));
1063 cut.addActionListener(new java.awt.event.ActionListener()
1065 public void actionPerformed(ActionEvent e)
1067 cut_actionPerformed(e);
1070 delete.setText("Delete");
1071 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1072 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1073 delete.addActionListener(new java.awt.event.ActionListener()
1075 public void actionPerformed(ActionEvent e)
1077 delete_actionPerformed(e);
1080 pasteMenu.setText("Paste");
1081 pasteNew.setText("To New Alignment");
1082 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1083 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1084 .getMenuShortcutKeyMask()
1085 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1086 pasteNew.addActionListener(new java.awt.event.ActionListener()
1088 public void actionPerformed(ActionEvent e)
1090 pasteNew_actionPerformed(e);
1093 pasteThis.setText("Add To This Alignment");
1094 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1095 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1096 .getMenuShortcutKeyMask(), false));
1097 pasteThis.addActionListener(new java.awt.event.ActionListener()
1099 public void actionPerformed(ActionEvent e)
1101 pasteThis_actionPerformed(e);
1104 applyToAllGroups.setText("Apply Colour To All Groups");
1105 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1107 public void actionPerformed(ActionEvent e)
1109 applyToAllGroups_actionPerformed(e);
1112 createPNG.addActionListener(new java.awt.event.ActionListener()
1114 public void actionPerformed(ActionEvent e)
1119 createPNG.setActionCommand("Save As PNG Image");
1120 createPNG.setText("PNG");
1121 font.setText("Font...");
1122 font.addActionListener(new java.awt.event.ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 font_actionPerformed(e);
1130 seqLimits.setText("Show Sequence Limits");
1131 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1132 seqLimits.addActionListener(new java.awt.event.ActionListener()
1134 public void actionPerformed(ActionEvent e)
1136 seqLimit_actionPerformed(e);
1139 epsFile.setText("EPS");
1140 epsFile.addActionListener(new java.awt.event.ActionListener()
1142 public void actionPerformed(ActionEvent e)
1147 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1148 LoadtreeMenuItem.setText("Load Associated Tree");
1149 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1151 public void actionPerformed(ActionEvent e)
1153 LoadtreeMenuItem_actionPerformed(e);
1156 scaleAbove.setVisible(false);
1157 scaleAbove.setText("Scale Above");
1158 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1160 public void actionPerformed(ActionEvent e)
1162 scaleAbove_actionPerformed(e);
1165 scaleLeft.setVisible(false);
1166 scaleLeft.setSelected(true);
1167 scaleLeft.setText("Scale Left");
1168 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1170 public void actionPerformed(ActionEvent e)
1172 scaleLeft_actionPerformed(e);
1175 scaleRight.setVisible(false);
1176 scaleRight.setSelected(true);
1177 scaleRight.setText("Scale Right");
1178 scaleRight.addActionListener(new java.awt.event.ActionListener()
1180 public void actionPerformed(ActionEvent e)
1182 scaleRight_actionPerformed(e);
1185 centreColumnLabelsMenuItem.setVisible(true);
1186 centreColumnLabelsMenuItem.setState(false);
1187 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1188 centreColumnLabelsMenuItem
1189 .addActionListener(new java.awt.event.ActionListener()
1191 public void actionPerformed(ActionEvent e)
1193 centreColumnLabels_actionPerformed(e);
1196 followHighlightMenuItem.setVisible(true);
1197 followHighlightMenuItem.setState(true);
1198 followHighlightMenuItem.setText("Automatic Scrolling");
1199 followHighlightMenuItem.addActionListener(new ActionListener()
1202 public void actionPerformed(ActionEvent e)
1204 followHighlight_actionPerformed();
1209 modifyPID.setText("Modify Identity Threshold...");
1210 modifyPID.addActionListener(new java.awt.event.ActionListener()
1212 public void actionPerformed(ActionEvent e)
1214 modifyPID_actionPerformed(e);
1217 modifyConservation.setText("Modify Conservation Threshold...");
1219 .addActionListener(new java.awt.event.ActionListener()
1221 public void actionPerformed(ActionEvent e)
1223 modifyConservation_actionPerformed(e);
1226 sortByTreeMenu.setText("By Tree Order");
1227 sort.setText("Sort");
1228 sort.addMenuListener(new MenuListener()
1230 public void menuSelected(MenuEvent e)
1235 public void menuDeselected(MenuEvent e)
1239 public void menuCanceled(MenuEvent e)
1243 sortByAnnotScore.setText("by Score");
1244 sort.add(sortByAnnotScore);
1245 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1248 public void menuCanceled(MenuEvent e)
1252 public void menuDeselected(MenuEvent e)
1256 public void menuSelected(MenuEvent e)
1258 buildSortByAnnotationScoresMenu();
1261 sortByAnnotScore.setVisible(false);
1263 calculateTree.setText("Calculate Tree");
1265 jMenu2.setText("Export Image");
1266 padGapsMenuitem.setText("Pad Gaps");
1267 padGapsMenuitem.setState(jalview.bin.Cache
1268 .getDefault("PAD_GAPS", false));
1269 padGapsMenuitem.addActionListener(new ActionListener()
1271 public void actionPerformed(ActionEvent e)
1273 padGapsMenuitem_actionPerformed(e);
1276 vamsasStore.setVisible(false);
1277 vamsasStore.setText("VAMSAS store");
1278 vamsasStore.addActionListener(new ActionListener()
1280 public void actionPerformed(ActionEvent e)
1282 vamsasStore_actionPerformed(e);
1285 showTranslation.setText("Translate cDNA");
1286 showTranslation.addActionListener(new ActionListener()
1288 public void actionPerformed(ActionEvent e)
1290 showTranslation_actionPerformed(e);
1293 extractScores.setText("Extract Scores...");
1294 extractScores.addActionListener(new ActionListener()
1296 public void actionPerformed(ActionEvent e)
1298 extractScores_actionPerformed(e);
1301 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1303 showProducts.setText("Get Cross References");
1305 * showProducts.addActionListener(new ActionListener() {
1307 * public void actionPerformed(ActionEvent e) {
1308 * showProducts_actionPerformed(e); } });
1310 featureSettings.setText("Feature Settings...");
1311 featureSettings.addActionListener(new ActionListener()
1313 public void actionPerformed(ActionEvent e)
1315 featureSettings_actionPerformed(e);
1318 fetchSequence.setText("Fetch Sequence(s)...");
1319 fetchSequence.addActionListener(new ActionListener()
1321 public void actionPerformed(ActionEvent e)
1323 fetchSequence_actionPerformed(e);
1327 annotationColour.setText("By Annotation...");
1328 annotationColour.addActionListener(new ActionListener()
1330 public void actionPerformed(ActionEvent e)
1332 annotationColour_actionPerformed(e);
1335 associatedData.setText("Load Features / Annotations");
1336 associatedData.addActionListener(new ActionListener()
1338 public void actionPerformed(ActionEvent e)
1340 associatedData_actionPerformed(e);
1343 autoCalculate.setText("Autocalculate Consensus");
1344 autoCalculate.setState(jalview.bin.Cache.getDefault(
1345 "AUTO_CALC_CONSENSUS", true));
1346 autoCalculate.addActionListener(new ActionListener()
1348 public void actionPerformed(ActionEvent e)
1350 autoCalculate_actionPerformed(e);
1353 addSequenceMenu.setText("Add Sequences");
1354 addFromFile.setText("From File");
1355 addFromFile.addActionListener(new ActionListener()
1357 public void actionPerformed(ActionEvent e)
1359 addFromFile_actionPerformed(e);
1362 addFromText.setText("From Textbox");
1363 addFromText.addActionListener(new ActionListener()
1365 public void actionPerformed(ActionEvent e)
1367 addFromText_actionPerformed(e);
1370 addFromURL.setText("From URL");
1371 addFromURL.addActionListener(new ActionListener()
1373 public void actionPerformed(ActionEvent e)
1375 addFromURL_actionPerformed(e);
1378 exportFeatures.setText("Export Features...");
1379 exportFeatures.addActionListener(new ActionListener()
1381 public void actionPerformed(ActionEvent e)
1383 exportFeatures_actionPerformed(e);
1386 exportAnnotations.setText("Export Annotations...");
1387 exportAnnotations.addActionListener(new ActionListener()
1389 public void actionPerformed(ActionEvent e)
1391 exportAnnotations_actionPerformed(e);
1394 statusPanel.setLayout(gridLayout1);
1395 jMenu3.setText("Show");
1396 showAllSeqs.setText("All Sequences");
1397 showAllSeqs.addActionListener(new ActionListener()
1399 public void actionPerformed(ActionEvent e)
1401 showAllSeqs_actionPerformed(e);
1404 showAllColumns.setText("All Columns");
1405 showAllColumns.addActionListener(new ActionListener()
1407 public void actionPerformed(ActionEvent e)
1409 showAllColumns_actionPerformed(e);
1412 hideMenu.setText("Hide");
1413 hideSelSequences.setText("Selected Sequences");
1414 hideSelSequences.addActionListener(new ActionListener()
1416 public void actionPerformed(ActionEvent e)
1418 hideSelSequences_actionPerformed(e);
1421 hideSelColumns.setText("Selected Columns");
1422 hideSelColumns.addActionListener(new ActionListener()
1424 public void actionPerformed(ActionEvent e)
1426 hideSelColumns_actionPerformed(e);
1429 hiddenMarkers.setText("Show Hidden Markers");
1430 hiddenMarkers.addActionListener(new ActionListener()
1432 public void actionPerformed(ActionEvent e)
1434 hiddenMarkers_actionPerformed(e);
1437 invertColSel.setText("Invert Column Selection");
1438 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1439 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1440 .getMenuShortcutKeyMask()
1441 | java.awt.event.KeyEvent.ALT_MASK, false));
1442 invertColSel.addActionListener(new ActionListener()
1444 public void actionPerformed(ActionEvent e)
1446 invertColSel_actionPerformed(e);
1449 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1451 public void stateChanged(ChangeEvent evt)
1453 JTabbedPane pane = (JTabbedPane) evt.getSource();
1454 int sel = pane.getSelectedIndex();
1455 tabSelectionChanged(sel);
1458 tabbedPane.addMouseListener(new MouseAdapter()
1460 public void mousePressed(MouseEvent e)
1462 tabbedPane_mousePressed(e);
1465 tabbedPane.addFocusListener(new FocusAdapter()
1467 public void focusGained(FocusEvent e)
1469 tabbedPane_focusGained(e);
1472 save.setText("Save");
1473 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1474 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1475 .getMenuShortcutKeyMask(), false));
1476 save.addActionListener(new ActionListener()
1478 public void actionPerformed(ActionEvent e)
1480 save_actionPerformed(e);
1483 reload.setEnabled(false);
1484 reload.setText("Reload");
1485 reload.addActionListener(new ActionListener()
1487 public void actionPerformed(ActionEvent e)
1489 reload_actionPerformed(e);
1492 newView.setText("New View");
1493 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1494 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1495 .getMenuShortcutKeyMask(), false));
1496 newView.addActionListener(new ActionListener()
1498 public void actionPerformed(ActionEvent e)
1500 newView_actionPerformed(e);
1503 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1504 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1505 textColour.setText("Colour Text ...");
1506 textColour.addActionListener(new ActionListener()
1508 public void actionPerformed(ActionEvent e)
1510 textColour_actionPerformed(e);
1513 formatMenu.setText("Format");
1514 selectMenu.setText("Select");
1515 idRightAlign.setText("Right Align Sequence Id");
1516 idRightAlign.addActionListener(new ActionListener()
1518 public void actionPerformed(ActionEvent e)
1520 idRightAlign_actionPerformed(e);
1523 gatherViews.setEnabled(false);
1524 gatherViews.setText("Gather Views");
1525 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1526 java.awt.event.KeyEvent.VK_G, 0, false));
1527 gatherViews.addActionListener(new ActionListener()
1529 public void actionPerformed(ActionEvent e)
1531 gatherViews_actionPerformed(e);
1534 expandViews.setEnabled(false);
1535 expandViews.setText("Expand Views");
1536 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1537 java.awt.event.KeyEvent.VK_X, 0, false));
1538 expandViews.addActionListener(new ActionListener()
1540 public void actionPerformed(ActionEvent e)
1542 expandViews_actionPerformed(e);
1545 pageSetup.setText("Page Setup ...");
1546 pageSetup.addActionListener(new ActionListener()
1548 public void actionPerformed(ActionEvent e)
1550 pageSetup_actionPerformed(e);
1553 alignmentProperties.setText("Alignment Properties...");
1554 alignmentProperties.addActionListener(new ActionListener()
1556 public void actionPerformed(ActionEvent actionEvent)
1558 alignmentProperties();
1561 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1562 alignFrameMenuBar.add(fileMenu);
1563 alignFrameMenuBar.add(editMenu);
1564 alignFrameMenuBar.add(selectMenu);
1565 alignFrameMenuBar.add(viewMenu);
1566 alignFrameMenuBar.add(formatMenu);
1567 alignFrameMenuBar.add(colourMenu);
1568 alignFrameMenuBar.add(calculateMenu);
1569 alignFrameMenuBar.add(webService);
1570 fileMenu.add(fetchSequence);
1571 fileMenu.add(addSequenceMenu);
1572 fileMenu.add(reload);
1573 fileMenu.addSeparator();
1574 fileMenu.add(vamsasStore);
1576 fileMenu.add(saveAs);
1577 fileMenu.add(outputTextboxMenu);
1578 fileMenu.add(pageSetup);
1579 fileMenu.add(printMenuItem);
1580 fileMenu.addSeparator();
1581 fileMenu.add(jMenu2);
1582 fileMenu.add(exportFeatures);
1583 fileMenu.add(exportAnnotations);
1584 fileMenu.add(LoadtreeMenuItem);
1585 fileMenu.add(associatedData);
1586 fileMenu.addSeparator();
1587 fileMenu.add(closeMenuItem);
1588 editMenu.add(undoMenuItem);
1589 editMenu.add(redoMenuItem);
1592 editMenu.add(pasteMenu);
1593 editMenu.add(delete);
1594 editMenu.addSeparator();
1595 editMenu.add(remove2LeftMenuItem);
1596 editMenu.add(remove2RightMenuItem);
1597 editMenu.add(removeGappedColumnMenuItem);
1598 editMenu.add(removeAllGapsMenuItem);
1599 editMenu.add(removeRedundancyMenuItem);
1600 editMenu.addSeparator();
1601 // dont add these yet in the CVS build - they cannot be undone!
1602 editMenu.add(justifyLeftMenuItem);
1603 editMenu.add(justifyRightMenuItem);
1604 editMenu.addSeparator();
1605 editMenu.add(padGapsMenuitem);
1606 viewMenu.add(newView);
1607 viewMenu.add(expandViews);
1608 viewMenu.add(gatherViews);
1609 viewMenu.addSeparator();
1610 viewMenu.add(jMenu3);
1611 viewMenu.add(hideMenu);
1612 viewMenu.addSeparator();
1613 viewMenu.add(followHighlightMenuItem);
1614 viewMenu.add(annotationPanelMenuItem);
1615 viewMenu.add(showGroupConservation);
1616 viewMenu.add(showGroupConsensus);
1617 viewMenu.addSeparator();
1618 viewMenu.add(showSeqFeatures);
1619 viewMenu.add(showSeqFeaturesHeight);
1621 viewMenu.add(featureSettings);
1622 tooltipSettingsMenu.add(showDbRefsMenuitem);
1623 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1624 viewMenu.add(tooltipSettingsMenu);
1625 viewMenu.addSeparator();
1626 viewMenu.add(alignmentProperties);
1627 viewMenu.addSeparator();
1628 viewMenu.add(overviewMenuItem);
1629 colourMenu.add(applyToAllGroups);
1630 colourMenu.add(textColour);
1631 colourMenu.addSeparator();
1632 colourMenu.add(noColourmenuItem);
1633 colourMenu.add(clustalColour);
1634 colourMenu.add(BLOSUM62Colour);
1635 colourMenu.add(PIDColour);
1636 colourMenu.add(zappoColour);
1637 colourMenu.add(taylorColour);
1638 colourMenu.add(hydrophobicityColour);
1639 colourMenu.add(helixColour);
1640 colourMenu.add(strandColour);
1641 colourMenu.add(turnColour);
1642 colourMenu.add(buriedColour);
1643 colourMenu.add(nucleotideColour);
1644 colourMenu.add(userDefinedColour);
1645 colourMenu.addSeparator();
1646 colourMenu.add(conservationMenuItem);
1647 colourMenu.add(modifyConservation);
1648 colourMenu.add(abovePIDThreshold);
1649 colourMenu.add(modifyPID);
1650 colourMenu.add(annotationColour);
1651 calculateMenu.add(sort);
1652 calculateMenu.add(calculateTree);
1653 calculateMenu.addSeparator();
1654 calculateMenu.add(pairwiseAlignmentMenuItem);
1655 calculateMenu.add(PCAMenuItem);
1656 calculateMenu.addSeparator();
1657 calculateMenu.add(showTranslation);
1658 calculateMenu.add(showProducts);
1659 calculateMenu.add(autoCalculate);
1660 calculateMenu.addSeparator();
1661 calculateMenu.add(extractScores);
1662 webServiceNoServices = new JMenuItem("<No Services>");
1663 webService.add(webServiceNoServices);
1664 pasteMenu.add(pasteNew);
1665 pasteMenu.add(pasteThis);
1666 sort.add(sortIDMenuItem);
1667 sort.add(sortLengthMenuItem);
1668 sort.add(sortGroupMenuItem);
1669 sort.add(sortPairwiseMenuItem);
1670 sort.add(sortByTreeMenu);
1671 calculateTree.add(averageDistanceTreeMenuItem);
1672 calculateTree.add(neighbourTreeMenuItem);
1673 calculateTree.add(avDistanceTreeBlosumMenuItem);
1674 calculateTree.add(njTreeBlosumMenuItem);
1675 jMenu2.add(htmlMenuItem);
1676 jMenu2.add(epsFile);
1677 jMenu2.add(createPNG);
1678 addSequenceMenu.add(addFromFile);
1679 addSequenceMenu.add(addFromText);
1680 addSequenceMenu.add(addFromURL);
1681 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1682 statusPanel.add(statusBar, null);
1683 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1684 jMenu3.add(showAllColumns);
1685 jMenu3.add(showAllSeqs);
1686 hideMenu.add(hideSelColumns);
1687 hideMenu.add(hideSelSequences);
1688 formatMenu.add(font);
1689 formatMenu.addSeparator();
1690 formatMenu.add(wrapMenuItem);
1691 formatMenu.add(scaleAbove);
1692 formatMenu.add(scaleLeft);
1693 formatMenu.add(scaleRight);
1694 formatMenu.add(seqLimits);
1695 formatMenu.add(idRightAlign);
1696 formatMenu.add(hiddenMarkers);
1697 formatMenu.add(viewBoxesMenuItem);
1698 formatMenu.add(viewTextMenuItem);
1699 formatMenu.add(colourTextMenuItem);
1700 formatMenu.add(renderGapsMenuItem);
1701 formatMenu.add(centreColumnLabelsMenuItem);
1702 formatMenu.add(showUnconservedMenuItem);
1703 selectMenu.add(findMenuItem);
1704 selectMenu.addSeparator();
1705 selectMenu.add(selectAllSequenceMenuItem);
1706 selectMenu.add(deselectAllSequenceMenuItem);
1707 selectMenu.add(invertSequenceMenuItem);
1708 selectMenu.add(invertColSel);
1709 selectMenu.add(deleteGroups);
1710 selectMenu.add(grpsFromSelection);
1713 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1715 // TODO Auto-generated method stub
1719 protected void showGroupConsensus_actionPerformed(ActionEvent e)
1721 // TODO Auto-generated method stub
1725 protected void showGroupConservation_actionPerformed(ActionEvent e)
1727 // TODO Auto-generated method stub
1731 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1733 // TODO Auto-generated method stub
1737 protected void showSeqFeaturesHeight_actionPerformed(
1738 ActionEvent actionEvent)
1740 // TODO Auto-generated method stub
1744 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1746 // TODO Auto-generated method stub
1750 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1752 // TODO Auto-generated method stub
1756 protected void followHighlight_actionPerformed()
1758 // TODO Auto-generated method stub
1762 protected void showNpFeats_actionPerformed(ActionEvent e)
1764 // TODO Auto-generated method stub
1768 protected void showDbRefs_actionPerformed(ActionEvent e)
1770 // TODO Auto-generated method stub
1774 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1778 protected void showProducts_actionPerformed(ActionEvent e)
1782 protected void buildSortByAnnotationScoresMenu()
1786 protected void extractScores_actionPerformed(ActionEvent e)
1790 protected void outputText_actionPerformed(ActionEvent e)
1794 public void addFromFile_actionPerformed(ActionEvent e)
1799 public void addFromText_actionPerformed(ActionEvent e)
1804 public void addFromURL_actionPerformed(ActionEvent e)
1809 public void exportFeatures_actionPerformed(ActionEvent e)
1814 public void exportAnnotations_actionPerformed(ActionEvent e)
1819 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1823 protected void closeMenuItem_actionPerformed(boolean b)
1827 protected void redoMenuItem_actionPerformed(ActionEvent e)
1831 protected void undoMenuItem_actionPerformed(ActionEvent e)
1835 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1839 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1843 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1847 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1851 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1855 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1859 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1863 protected void wrapMenuItem_actionPerformed(ActionEvent e)
1867 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1871 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1875 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1879 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1883 protected void overviewMenuItem_actionPerformed(ActionEvent e)
1887 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1891 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1895 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
1899 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1903 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1907 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1911 protected void PCAMenuItem_actionPerformed(ActionEvent e)
1915 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1919 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1923 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1927 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1931 protected void clustalColour_actionPerformed(ActionEvent e)
1935 protected void zappoColour_actionPerformed(ActionEvent e)
1939 protected void taylorColour_actionPerformed(ActionEvent e)
1943 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1947 protected void helixColour_actionPerformed(ActionEvent e)
1951 protected void strandColour_actionPerformed(ActionEvent e)
1955 protected void turnColour_actionPerformed(ActionEvent e)
1959 protected void buriedColour_actionPerformed(ActionEvent e)
1963 protected void userDefinedColour_actionPerformed(ActionEvent e)
1967 protected void PIDColour_actionPerformed(ActionEvent e)
1971 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1975 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1979 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1983 protected void printMenuItem_actionPerformed(ActionEvent e)
1987 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1991 protected void findMenuItem_actionPerformed(ActionEvent e)
1995 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1999 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2003 protected void nucleotideColour_actionPerformed(ActionEvent e)
2007 protected void deleteGroups_actionPerformed(ActionEvent e)
2011 protected void copy_actionPerformed(ActionEvent e)
2015 protected void cut_actionPerformed(ActionEvent e)
2019 protected void delete_actionPerformed(ActionEvent e)
2023 protected void pasteNew_actionPerformed(ActionEvent e)
2027 protected void pasteThis_actionPerformed(ActionEvent e)
2031 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2035 public void createPNG(java.io.File f)
2039 protected void font_actionPerformed(ActionEvent e)
2043 protected void seqLimit_actionPerformed(ActionEvent e)
2047 public void seqDBRef_actionPerformed(ActionEvent e)
2052 public void createEPS(java.io.File f)
2056 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2060 protected void jpred_actionPerformed(ActionEvent e)
2064 protected void scaleAbove_actionPerformed(ActionEvent e)
2068 protected void scaleLeft_actionPerformed(ActionEvent e)
2072 protected void scaleRight_actionPerformed(ActionEvent e)
2076 protected void modifyPID_actionPerformed(ActionEvent e)
2080 protected void modifyConservation_actionPerformed(ActionEvent e)
2084 protected void saveAs_actionPerformed(ActionEvent e)
2088 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2092 public void vamsasStore_actionPerformed(ActionEvent e)
2097 public void vamsasLoad_actionPerformed(ActionEvent e)
2102 public void showTranslation_actionPerformed(ActionEvent e)
2107 public void featureSettings_actionPerformed(ActionEvent e)
2112 public void fetchSequence_actionPerformed(ActionEvent e)
2117 public void smoothFont_actionPerformed(ActionEvent e)
2122 public void annotationColour_actionPerformed(ActionEvent e)
2127 public void associatedData_actionPerformed(ActionEvent e)
2132 public void autoCalculate_actionPerformed(ActionEvent e)
2137 public void showAllSeqs_actionPerformed(ActionEvent e)
2142 public void showAllColumns_actionPerformed(ActionEvent e)
2147 public void hideSelSequences_actionPerformed(ActionEvent e)
2152 public void hideSelColumns_actionPerformed(ActionEvent e)
2157 public void hiddenMarkers_actionPerformed(ActionEvent e)
2162 public void findPdbId_actionPerformed(ActionEvent e)
2167 public void enterPdbId_actionPerformed(ActionEvent e)
2172 public void pdbFile_actionPerformed(ActionEvent e)
2177 public void invertColSel_actionPerformed(ActionEvent e)
2182 public void tabSelectionChanged(int sel)
2187 public void tabbedPane_mousePressed(MouseEvent e)
2192 public void tabbedPane_focusGained(FocusEvent e)
2197 public void save_actionPerformed(ActionEvent e)
2202 public void reload_actionPerformed(ActionEvent e)
2207 public void newView_actionPerformed(ActionEvent e)
2212 public void textColour_actionPerformed(ActionEvent e)
2217 public void idRightAlign_actionPerformed(ActionEvent e)
2222 public void expandViews_actionPerformed(ActionEvent e)
2227 public void gatherViews_actionPerformed(ActionEvent e)
2232 public void buildTreeMenu()
2237 public void pageSetup_actionPerformed(ActionEvent e)
2242 public void alignmentProperties()