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();
296 setJMenuBar(alignFrameMenuBar);
298 // dynamically fill save as menu with available formats
299 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
301 JMenuItem item = new JMenuItem(
302 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
304 item.addActionListener(new java.awt.event.ActionListener()
306 public void actionPerformed(ActionEvent e)
308 outputText_actionPerformed(e);
312 outputTextboxMenu.add(item);
314 } catch (Exception e)
318 if (!new jalview.util.Platform().isAMac())
320 closeMenuItem.setMnemonic('C');
321 outputTextboxMenu.setMnemonic('T');
322 undoMenuItem.setMnemonic('Z');
323 redoMenuItem.setMnemonic('0');
324 copy.setMnemonic('C');
325 cut.setMnemonic('U');
326 pasteMenu.setMnemonic('P');
327 reload.setMnemonic('R');
330 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
332 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
333 .getUserColourSchemes().keys();
335 while (userColours.hasMoreElements())
337 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
338 userColours.nextElement().toString());
339 radioItem.setName("USER_DEFINED");
340 radioItem.addMouseListener(new MouseAdapter()
342 public void mousePressed(MouseEvent evt)
344 if (evt.isControlDown()
345 || SwingUtilities.isRightMouseButton(evt))
348 .removeActionListener(radioItem.getActionListeners()[0]);
350 int option = JOptionPane.showInternalConfirmDialog(
351 jalview.gui.Desktop.desktop,
352 "Remove from default list?",
353 "Remove user defined colour",
354 JOptionPane.YES_NO_OPTION);
355 if (option == JOptionPane.YES_OPTION)
357 jalview.gui.UserDefinedColours
358 .removeColourFromDefaults(radioItem.getText());
359 colourMenu.remove(radioItem);
363 radioItem.addActionListener(new ActionListener()
365 public void actionPerformed(ActionEvent evt)
367 userDefinedColour_actionPerformed(evt);
374 radioItem.addActionListener(new ActionListener()
376 public void actionPerformed(ActionEvent evt)
378 userDefinedColour_actionPerformed(evt);
381 colourMenu.insert(radioItem, 15);
382 colours.add(radioItem);
385 colours.add(noColourmenuItem);
386 colours.add(clustalColour);
387 colours.add(zappoColour);
388 colours.add(taylorColour);
389 colours.add(hydrophobicityColour);
390 colours.add(helixColour);
391 colours.add(strandColour);
392 colours.add(turnColour);
393 colours.add(buriedColour);
394 colours.add(userDefinedColour);
395 colours.add(PIDColour);
396 colours.add(BLOSUM62Colour);
397 colours.add(nucleotideColour);
399 setColourSelected(jalview.bin.Cache
400 .getDefault("DEFAULT_COLOUR", "None"));
404 public void setColourSelected(String defaultColour)
407 if (defaultColour != null)
409 int index = ColourSchemeProperty
410 .getColourIndexFromName(defaultColour);
414 case ColourSchemeProperty.NONE:
415 noColourmenuItem.setSelected(true);
417 case ColourSchemeProperty.CLUSTAL:
418 clustalColour.setSelected(true);
422 case ColourSchemeProperty.BLOSUM:
423 BLOSUM62Colour.setSelected(true);
427 case ColourSchemeProperty.PID:
428 PIDColour.setSelected(true);
432 case ColourSchemeProperty.ZAPPO:
433 zappoColour.setSelected(true);
437 case ColourSchemeProperty.TAYLOR:
438 taylorColour.setSelected(true);
441 case ColourSchemeProperty.HYDROPHOBIC:
442 hydrophobicityColour.setSelected(true);
446 case ColourSchemeProperty.HELIX:
447 helixColour.setSelected(true);
451 case ColourSchemeProperty.STRAND:
452 strandColour.setSelected(true);
456 case ColourSchemeProperty.TURN:
457 turnColour.setSelected(true);
461 case ColourSchemeProperty.BURIED:
462 buriedColour.setSelected(true);
466 case ColourSchemeProperty.NUCLEOTIDE:
467 nucleotideColour.setSelected(true);
471 case ColourSchemeProperty.USER_DEFINED:
472 userDefinedColour.setSelected(true);
480 private void jbInit() throws Exception
482 fileMenu.setText("File");
483 saveAs.setText("Save As...");
484 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
485 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
486 .getMenuShortcutKeyMask()
487 | java.awt.event.KeyEvent.SHIFT_MASK, false));
488 saveAs.addActionListener(new ActionListener()
490 public void actionPerformed(ActionEvent e)
492 saveAs_actionPerformed(e);
495 closeMenuItem.setText("Close");
496 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
497 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
498 .getMenuShortcutKeyMask(), false));
499 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
501 public void actionPerformed(ActionEvent e)
503 closeMenuItem_actionPerformed(false);
506 editMenu.setText("Edit");
507 viewMenu.setText("View");
508 colourMenu.setText("Colour");
509 calculateMenu.setText("Calculate");
510 webService.setText("Web Service");
511 selectAllSequenceMenuItem.setText("Select All");
512 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
513 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
514 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
515 selectAllSequenceMenuItem
516 .addActionListener(new java.awt.event.ActionListener()
518 public void actionPerformed(ActionEvent e)
520 selectAllSequenceMenuItem_actionPerformed(e);
523 deselectAllSequenceMenuItem.setText("Deselect All");
524 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
525 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
526 deselectAllSequenceMenuItem
527 .addActionListener(new java.awt.event.ActionListener()
529 public void actionPerformed(ActionEvent e)
531 deselectAllSequenceMenuItem_actionPerformed(e);
534 invertSequenceMenuItem.setText("Invert Sequence Selection");
535 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
536 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
537 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
538 invertSequenceMenuItem
539 .addActionListener(new java.awt.event.ActionListener()
541 public void actionPerformed(ActionEvent e)
543 invertSequenceMenuItem_actionPerformed(e);
546 remove2LeftMenuItem.setText("Remove Left");
547 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
548 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
549 .getMenuShortcutKeyMask(), false));
551 .addActionListener(new java.awt.event.ActionListener()
553 public void actionPerformed(ActionEvent e)
555 remove2LeftMenuItem_actionPerformed(e);
558 remove2RightMenuItem.setText("Remove Right");
559 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
560 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
561 .getMenuShortcutKeyMask(), false));
563 .addActionListener(new java.awt.event.ActionListener()
565 public void actionPerformed(ActionEvent e)
567 remove2RightMenuItem_actionPerformed(e);
570 removeGappedColumnMenuItem.setText("Remove Empty Columns");
571 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
572 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
573 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
574 removeGappedColumnMenuItem
575 .addActionListener(new java.awt.event.ActionListener()
577 public void actionPerformed(ActionEvent e)
579 removeGappedColumnMenuItem_actionPerformed(e);
582 removeAllGapsMenuItem.setText("Remove All Gaps");
583 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
584 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
585 .getDefaultToolkit().getMenuShortcutKeyMask()
586 | java.awt.event.KeyEvent.SHIFT_MASK, false));
587 removeAllGapsMenuItem
588 .addActionListener(new java.awt.event.ActionListener()
590 public void actionPerformed(ActionEvent e)
592 removeAllGapsMenuItem_actionPerformed(e);
595 justifyLeftMenuItem.setText("Left Justify Alignment");
596 justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
598 public void actionPerformed(ActionEvent e)
600 justifyLeftMenuItem_actionPerformed(e);
603 justifyRightMenuItem.setText("Right Justify Alignment");
604 justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
606 public void actionPerformed(ActionEvent e)
608 justifyRightMenuItem_actionPerformed(e);
611 viewBoxesMenuItem.setText("Boxes");
612 viewBoxesMenuItem.setState(true);
613 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
615 public void actionPerformed(ActionEvent e)
617 viewBoxesMenuItem_actionPerformed(e);
620 viewTextMenuItem.setText("Text");
621 viewTextMenuItem.setState(true);
622 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
624 public void actionPerformed(ActionEvent e)
626 viewTextMenuItem_actionPerformed(e);
629 showUnconservedMenuItem.setText("Show Unconserved");
630 showUnconservedMenuItem.setState(false);
631 showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
633 public void actionPerformed(ActionEvent e)
635 showUnconservedMenuItem_actionPerformed(e);
638 sortPairwiseMenuItem.setText("by Pairwise Identity");
640 .addActionListener(new java.awt.event.ActionListener()
642 public void actionPerformed(ActionEvent e)
644 sortPairwiseMenuItem_actionPerformed(e);
647 sortIDMenuItem.setText("by ID");
648 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
650 public void actionPerformed(ActionEvent e)
652 sortIDMenuItem_actionPerformed(e);
655 sortLengthMenuItem.setText("By Length");
656 sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
658 public void actionPerformed(ActionEvent e)
660 sortLengthMenuItem_actionPerformed(e);
663 sortGroupMenuItem.setText("by Group");
664 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
666 public void actionPerformed(ActionEvent e)
668 sortGroupMenuItem_actionPerformed(e);
671 removeRedundancyMenuItem.setText("Remove Redundancy...");
672 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
673 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
674 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
675 removeRedundancyMenuItem
676 .addActionListener(new java.awt.event.ActionListener()
678 public void actionPerformed(ActionEvent e)
680 removeRedundancyMenuItem_actionPerformed(e);
683 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
684 pairwiseAlignmentMenuItem
685 .addActionListener(new java.awt.event.ActionListener()
687 public void actionPerformed(ActionEvent e)
689 pairwiseAlignmentMenuItem_actionPerformed(e);
692 PCAMenuItem.setText("Principal Component Analysis");
693 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
695 public void actionPerformed(ActionEvent e)
697 PCAMenuItem_actionPerformed(e);
700 averageDistanceTreeMenuItem
701 .setText("Average Distance Using % Identity");
702 averageDistanceTreeMenuItem
703 .addActionListener(new java.awt.event.ActionListener()
705 public void actionPerformed(ActionEvent e)
707 averageDistanceTreeMenuItem_actionPerformed(e);
710 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
711 neighbourTreeMenuItem
712 .addActionListener(new java.awt.event.ActionListener()
714 public void actionPerformed(ActionEvent e)
716 neighbourTreeMenuItem_actionPerformed(e);
719 this.getContentPane().setLayout(borderLayout1);
720 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
721 statusBar.setBackground(Color.white);
722 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
723 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
724 statusBar.setText("Status bar");
725 outputTextboxMenu.setText("Output to Textbox");
726 clustalColour.setText("Clustalx");
728 clustalColour.addActionListener(new java.awt.event.ActionListener()
730 public void actionPerformed(ActionEvent e)
732 clustalColour_actionPerformed(e);
735 zappoColour.setText("Zappo");
736 zappoColour.addActionListener(new java.awt.event.ActionListener()
738 public void actionPerformed(ActionEvent e)
740 zappoColour_actionPerformed(e);
743 taylorColour.setText("Taylor");
744 taylorColour.addActionListener(new java.awt.event.ActionListener()
746 public void actionPerformed(ActionEvent e)
748 taylorColour_actionPerformed(e);
751 hydrophobicityColour.setText("Hydrophobicity");
753 .addActionListener(new java.awt.event.ActionListener()
755 public void actionPerformed(ActionEvent e)
757 hydrophobicityColour_actionPerformed(e);
760 helixColour.setText("Helix Propensity");
761 helixColour.addActionListener(new java.awt.event.ActionListener()
763 public void actionPerformed(ActionEvent e)
765 helixColour_actionPerformed(e);
768 strandColour.setText("Strand Propensity");
769 strandColour.addActionListener(new java.awt.event.ActionListener()
771 public void actionPerformed(ActionEvent e)
773 strandColour_actionPerformed(e);
776 turnColour.setText("Turn Propensity");
777 turnColour.addActionListener(new java.awt.event.ActionListener()
779 public void actionPerformed(ActionEvent e)
781 turnColour_actionPerformed(e);
784 buriedColour.setText("Buried Index");
785 buriedColour.addActionListener(new java.awt.event.ActionListener()
787 public void actionPerformed(ActionEvent e)
789 buriedColour_actionPerformed(e);
792 userDefinedColour.setText("User Defined...");
793 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
795 public void actionPerformed(ActionEvent e)
797 userDefinedColour_actionPerformed(e);
800 PIDColour.setText("Percentage Identity");
801 PIDColour.addActionListener(new java.awt.event.ActionListener()
803 public void actionPerformed(ActionEvent e)
805 PIDColour_actionPerformed(e);
808 BLOSUM62Colour.setText("BLOSUM62 Score");
809 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
811 public void actionPerformed(ActionEvent e)
813 BLOSUM62Colour_actionPerformed(e);
816 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
817 avDistanceTreeBlosumMenuItem
818 .addActionListener(new java.awt.event.ActionListener()
820 public void actionPerformed(ActionEvent e)
822 avTreeBlosumMenuItem_actionPerformed(e);
825 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
827 .addActionListener(new java.awt.event.ActionListener()
829 public void actionPerformed(ActionEvent e)
831 njTreeBlosumMenuItem_actionPerformed(e);
834 annotationPanelMenuItem.setActionCommand("");
835 annotationPanelMenuItem.setText("Show Annotations");
836 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
837 "SHOW_ANNOTATIONS", true));
838 annotationPanelMenuItem
839 .addActionListener(new java.awt.event.ActionListener()
841 public void actionPerformed(ActionEvent e)
843 annotationPanelMenuItem_actionPerformed(e);
846 colourTextMenuItem.setText("Colour Text");
848 .addActionListener(new java.awt.event.ActionListener()
850 public void actionPerformed(ActionEvent e)
852 colourTextMenuItem_actionPerformed(e);
855 htmlMenuItem.setText("HTML");
856 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
858 public void actionPerformed(ActionEvent e)
860 htmlMenuItem_actionPerformed(e);
863 overviewMenuItem.setText("Overview Window");
864 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
866 public void actionPerformed(ActionEvent e)
868 overviewMenuItem_actionPerformed(e);
871 undoMenuItem.setEnabled(false);
872 undoMenuItem.setText("Undo");
873 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
874 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
875 .getMenuShortcutKeyMask(), false));
876 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
878 public void actionPerformed(ActionEvent e)
880 undoMenuItem_actionPerformed(e);
883 redoMenuItem.setEnabled(false);
884 redoMenuItem.setText("Redo");
885 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
886 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
887 .getMenuShortcutKeyMask(), false));
888 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
890 public void actionPerformed(ActionEvent e)
892 redoMenuItem_actionPerformed(e);
895 conservationMenuItem.setText("By Conservation");
897 .addActionListener(new java.awt.event.ActionListener()
899 public void actionPerformed(ActionEvent e)
901 conservationMenuItem_actionPerformed(e);
904 noColourmenuItem.setText("None");
905 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
907 public void actionPerformed(ActionEvent e)
909 noColourmenuItem_actionPerformed(e);
912 wrapMenuItem.setText("Wrap");
913 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
915 public void actionPerformed(ActionEvent e)
917 wrapMenuItem_actionPerformed(e);
920 printMenuItem.setText("Print ...");
921 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
922 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
923 .getMenuShortcutKeyMask(), false));
924 printMenuItem.addActionListener(new java.awt.event.ActionListener()
926 public void actionPerformed(ActionEvent e)
928 printMenuItem_actionPerformed(e);
931 renderGapsMenuItem.setText("Show Gaps");
932 renderGapsMenuItem.setState(true);
934 .addActionListener(new java.awt.event.ActionListener()
936 public void actionPerformed(ActionEvent e)
938 renderGapsMenuItem_actionPerformed(e);
941 findMenuItem.setText("Find...");
942 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
943 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
944 .getMenuShortcutKeyMask(), false));
945 findMenuItem.addActionListener(new java.awt.event.ActionListener()
947 public void actionPerformed(ActionEvent e)
949 findMenuItem_actionPerformed(e);
952 abovePIDThreshold.setText("Above Identity Threshold");
953 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
955 public void actionPerformed(ActionEvent e)
957 abovePIDThreshold_actionPerformed(e);
960 showSeqFeatures.setText("Show Sequence Features");
961 showSeqFeatures.addActionListener(new ActionListener()
963 public void actionPerformed(ActionEvent actionEvent)
965 showSeqFeatures_actionPerformed(actionEvent);
968 showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
969 showSeqFeaturesHeight.addActionListener(new ActionListener()
971 public void actionPerformed(ActionEvent actionEvent)
973 showSeqFeaturesHeight_actionPerformed(actionEvent);
976 showDbRefsMenuitem.setText("Show Database Refs");
977 showDbRefsMenuitem.addActionListener(new ActionListener()
980 public void actionPerformed(ActionEvent e)
982 showDbRefs_actionPerformed(e);
986 showNpFeatsMenuitem.setText("Show Non-Positional Features");
987 showNpFeatsMenuitem.addActionListener(new ActionListener()
990 public void actionPerformed(ActionEvent e)
992 showNpFeats_actionPerformed(e);
996 showGroupConservation.setText("Group Conservation");
997 showGroupConservation.addActionListener(new ActionListener()
1000 public void actionPerformed(ActionEvent e)
1002 showGroupConservation_actionPerformed(e);
1007 showGroupConsensus.setText("Group Consensus");
1008 showGroupConsensus.addActionListener(new ActionListener()
1011 public void actionPerformed(ActionEvent e)
1013 showGroupConsensus_actionPerformed(e);
1018 nucleotideColour.setText("Nucleotide");
1019 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1021 public void actionPerformed(ActionEvent e)
1023 nucleotideColour_actionPerformed(e);
1026 deleteGroups.setText("Undefine groups");
1027 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1028 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1029 .getMenuShortcutKeyMask(), false));
1030 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1032 public void actionPerformed(ActionEvent e)
1034 deleteGroups_actionPerformed(e);
1037 copy.setText("Copy");
1038 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1039 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1040 .getMenuShortcutKeyMask(), false));
1042 copy.addActionListener(new java.awt.event.ActionListener()
1044 public void actionPerformed(ActionEvent e)
1046 copy_actionPerformed(e);
1050 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1051 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1052 .getMenuShortcutKeyMask(), false));
1053 cut.addActionListener(new java.awt.event.ActionListener()
1055 public void actionPerformed(ActionEvent e)
1057 cut_actionPerformed(e);
1060 delete.setText("Delete");
1061 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1062 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1063 delete.addActionListener(new java.awt.event.ActionListener()
1065 public void actionPerformed(ActionEvent e)
1067 delete_actionPerformed(e);
1070 pasteMenu.setText("Paste");
1071 pasteNew.setText("To New Alignment");
1072 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1073 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1074 .getMenuShortcutKeyMask()
1075 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1076 pasteNew.addActionListener(new java.awt.event.ActionListener()
1078 public void actionPerformed(ActionEvent e)
1080 pasteNew_actionPerformed(e);
1083 pasteThis.setText("Add To This Alignment");
1084 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1085 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1086 .getMenuShortcutKeyMask(), false));
1087 pasteThis.addActionListener(new java.awt.event.ActionListener()
1089 public void actionPerformed(ActionEvent e)
1091 pasteThis_actionPerformed(e);
1094 applyToAllGroups.setText("Apply Colour To All Groups");
1095 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1097 public void actionPerformed(ActionEvent e)
1099 applyToAllGroups_actionPerformed(e);
1102 createPNG.addActionListener(new java.awt.event.ActionListener()
1104 public void actionPerformed(ActionEvent e)
1109 createPNG.setActionCommand("Save As PNG Image");
1110 createPNG.setText("PNG");
1111 font.setText("Font...");
1112 font.addActionListener(new java.awt.event.ActionListener()
1114 public void actionPerformed(ActionEvent e)
1116 font_actionPerformed(e);
1120 seqLimits.setText("Show Sequence Limits");
1121 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1122 seqLimits.addActionListener(new java.awt.event.ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 seqLimit_actionPerformed(e);
1129 epsFile.setText("EPS");
1130 epsFile.addActionListener(new java.awt.event.ActionListener()
1132 public void actionPerformed(ActionEvent e)
1137 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1138 LoadtreeMenuItem.setText("Load Associated Tree");
1139 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1141 public void actionPerformed(ActionEvent e)
1143 LoadtreeMenuItem_actionPerformed(e);
1146 scaleAbove.setVisible(false);
1147 scaleAbove.setText("Scale Above");
1148 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1150 public void actionPerformed(ActionEvent e)
1152 scaleAbove_actionPerformed(e);
1155 scaleLeft.setVisible(false);
1156 scaleLeft.setSelected(true);
1157 scaleLeft.setText("Scale Left");
1158 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1160 public void actionPerformed(ActionEvent e)
1162 scaleLeft_actionPerformed(e);
1165 scaleRight.setVisible(false);
1166 scaleRight.setSelected(true);
1167 scaleRight.setText("Scale Right");
1168 scaleRight.addActionListener(new java.awt.event.ActionListener()
1170 public void actionPerformed(ActionEvent e)
1172 scaleRight_actionPerformed(e);
1175 centreColumnLabelsMenuItem.setVisible(true);
1176 centreColumnLabelsMenuItem.setState(false);
1177 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1178 centreColumnLabelsMenuItem
1179 .addActionListener(new java.awt.event.ActionListener()
1181 public void actionPerformed(ActionEvent e)
1183 centreColumnLabels_actionPerformed(e);
1186 followHighlightMenuItem.setVisible(true);
1187 followHighlightMenuItem.setState(true);
1188 followHighlightMenuItem.setText("Automatic Scrolling");
1189 followHighlightMenuItem.addActionListener(new ActionListener()
1192 public void actionPerformed(ActionEvent e)
1194 followHighlight_actionPerformed();
1199 modifyPID.setText("Modify Identity Threshold...");
1200 modifyPID.addActionListener(new java.awt.event.ActionListener()
1202 public void actionPerformed(ActionEvent e)
1204 modifyPID_actionPerformed(e);
1207 modifyConservation.setText("Modify Conservation Threshold...");
1209 .addActionListener(new java.awt.event.ActionListener()
1211 public void actionPerformed(ActionEvent e)
1213 modifyConservation_actionPerformed(e);
1216 sortByTreeMenu.setText("By Tree Order");
1217 sort.setText("Sort");
1218 sort.addMenuListener(new MenuListener()
1220 public void menuSelected(MenuEvent e)
1225 public void menuDeselected(MenuEvent e)
1229 public void menuCanceled(MenuEvent e)
1233 sortByAnnotScore.setText("by Score");
1234 sort.add(sortByAnnotScore);
1235 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1238 public void menuCanceled(MenuEvent e)
1242 public void menuDeselected(MenuEvent e)
1246 public void menuSelected(MenuEvent e)
1248 buildSortByAnnotationScoresMenu();
1251 sortByAnnotScore.setVisible(false);
1253 calculateTree.setText("Calculate Tree");
1255 jMenu2.setText("Export Image");
1256 padGapsMenuitem.setText("Pad Gaps");
1257 padGapsMenuitem.setState(jalview.bin.Cache
1258 .getDefault("PAD_GAPS", false));
1259 padGapsMenuitem.addActionListener(new ActionListener()
1261 public void actionPerformed(ActionEvent e)
1263 padGapsMenuitem_actionPerformed(e);
1266 vamsasStore.setVisible(false);
1267 vamsasStore.setText("VAMSAS store");
1268 vamsasStore.addActionListener(new ActionListener()
1270 public void actionPerformed(ActionEvent e)
1272 vamsasStore_actionPerformed(e);
1275 showTranslation.setText("Translate cDNA");
1276 showTranslation.addActionListener(new ActionListener()
1278 public void actionPerformed(ActionEvent e)
1280 showTranslation_actionPerformed(e);
1283 extractScores.setText("Extract Scores...");
1284 extractScores.addActionListener(new ActionListener()
1286 public void actionPerformed(ActionEvent e)
1288 extractScores_actionPerformed(e);
1291 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1293 showProducts.setText("Get Cross References");
1295 * showProducts.addActionListener(new ActionListener() {
1297 * public void actionPerformed(ActionEvent e) {
1298 * showProducts_actionPerformed(e); } });
1300 featureSettings.setText("Feature Settings...");
1301 featureSettings.addActionListener(new ActionListener()
1303 public void actionPerformed(ActionEvent e)
1305 featureSettings_actionPerformed(e);
1308 fetchSequence.setText("Fetch Sequence(s)...");
1309 fetchSequence.addActionListener(new ActionListener()
1311 public void actionPerformed(ActionEvent e)
1313 fetchSequence_actionPerformed(e);
1317 annotationColour.setText("By Annotation...");
1318 annotationColour.addActionListener(new ActionListener()
1320 public void actionPerformed(ActionEvent e)
1322 annotationColour_actionPerformed(e);
1325 associatedData.setText("Load Features / Annotations");
1326 associatedData.addActionListener(new ActionListener()
1328 public void actionPerformed(ActionEvent e)
1330 associatedData_actionPerformed(e);
1333 autoCalculate.setText("Autocalculate Consensus");
1334 autoCalculate.setState(jalview.bin.Cache.getDefault(
1335 "AUTO_CALC_CONSENSUS", true));
1336 autoCalculate.addActionListener(new ActionListener()
1338 public void actionPerformed(ActionEvent e)
1340 autoCalculate_actionPerformed(e);
1343 addSequenceMenu.setText("Add Sequences");
1344 addFromFile.setText("From File");
1345 addFromFile.addActionListener(new ActionListener()
1347 public void actionPerformed(ActionEvent e)
1349 addFromFile_actionPerformed(e);
1352 addFromText.setText("From Textbox");
1353 addFromText.addActionListener(new ActionListener()
1355 public void actionPerformed(ActionEvent e)
1357 addFromText_actionPerformed(e);
1360 addFromURL.setText("From URL");
1361 addFromURL.addActionListener(new ActionListener()
1363 public void actionPerformed(ActionEvent e)
1365 addFromURL_actionPerformed(e);
1368 exportFeatures.setText("Export Features...");
1369 exportFeatures.addActionListener(new ActionListener()
1371 public void actionPerformed(ActionEvent e)
1373 exportFeatures_actionPerformed(e);
1376 exportAnnotations.setText("Export Annotations...");
1377 exportAnnotations.addActionListener(new ActionListener()
1379 public void actionPerformed(ActionEvent e)
1381 exportAnnotations_actionPerformed(e);
1384 statusPanel.setLayout(gridLayout1);
1385 jMenu3.setText("Show");
1386 showAllSeqs.setText("All Sequences");
1387 showAllSeqs.addActionListener(new ActionListener()
1389 public void actionPerformed(ActionEvent e)
1391 showAllSeqs_actionPerformed(e);
1394 showAllColumns.setText("All Columns");
1395 showAllColumns.addActionListener(new ActionListener()
1397 public void actionPerformed(ActionEvent e)
1399 showAllColumns_actionPerformed(e);
1402 hideMenu.setText("Hide");
1403 hideSelSequences.setText("Selected Sequences");
1404 hideSelSequences.addActionListener(new ActionListener()
1406 public void actionPerformed(ActionEvent e)
1408 hideSelSequences_actionPerformed(e);
1411 hideSelColumns.setText("Selected Columns");
1412 hideSelColumns.addActionListener(new ActionListener()
1414 public void actionPerformed(ActionEvent e)
1416 hideSelColumns_actionPerformed(e);
1419 hiddenMarkers.setText("Show Hidden Markers");
1420 hiddenMarkers.addActionListener(new ActionListener()
1422 public void actionPerformed(ActionEvent e)
1424 hiddenMarkers_actionPerformed(e);
1427 invertColSel.setText("Invert Column Selection");
1428 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1429 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1430 .getMenuShortcutKeyMask()
1431 | java.awt.event.KeyEvent.ALT_MASK, false));
1432 invertColSel.addActionListener(new ActionListener()
1434 public void actionPerformed(ActionEvent e)
1436 invertColSel_actionPerformed(e);
1439 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1441 public void stateChanged(ChangeEvent evt)
1443 JTabbedPane pane = (JTabbedPane) evt.getSource();
1444 int sel = pane.getSelectedIndex();
1445 tabSelectionChanged(sel);
1448 tabbedPane.addMouseListener(new MouseAdapter()
1450 public void mousePressed(MouseEvent e)
1452 tabbedPane_mousePressed(e);
1455 tabbedPane.addFocusListener(new FocusAdapter()
1457 public void focusGained(FocusEvent e)
1459 tabbedPane_focusGained(e);
1462 save.setText("Save");
1463 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1464 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1465 .getMenuShortcutKeyMask(), false));
1466 save.addActionListener(new ActionListener()
1468 public void actionPerformed(ActionEvent e)
1470 save_actionPerformed(e);
1473 reload.setEnabled(false);
1474 reload.setText("Reload");
1475 reload.addActionListener(new ActionListener()
1477 public void actionPerformed(ActionEvent e)
1479 reload_actionPerformed(e);
1482 newView.setText("New View");
1483 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1484 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1485 .getMenuShortcutKeyMask(), false));
1486 newView.addActionListener(new ActionListener()
1488 public void actionPerformed(ActionEvent e)
1490 newView_actionPerformed(e);
1493 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1494 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1495 textColour.setText("Colour Text ...");
1496 textColour.addActionListener(new ActionListener()
1498 public void actionPerformed(ActionEvent e)
1500 textColour_actionPerformed(e);
1503 formatMenu.setText("Format");
1504 selectMenu.setText("Select");
1505 idRightAlign.setText("Right Align Sequence Id");
1506 idRightAlign.addActionListener(new ActionListener()
1508 public void actionPerformed(ActionEvent e)
1510 idRightAlign_actionPerformed(e);
1513 gatherViews.setEnabled(false);
1514 gatherViews.setText("Gather Views");
1515 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1516 java.awt.event.KeyEvent.VK_G, 0, false));
1517 gatherViews.addActionListener(new ActionListener()
1519 public void actionPerformed(ActionEvent e)
1521 gatherViews_actionPerformed(e);
1524 expandViews.setEnabled(false);
1525 expandViews.setText("Expand Views");
1526 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1527 java.awt.event.KeyEvent.VK_X, 0, false));
1528 expandViews.addActionListener(new ActionListener()
1530 public void actionPerformed(ActionEvent e)
1532 expandViews_actionPerformed(e);
1535 pageSetup.setText("Page Setup ...");
1536 pageSetup.addActionListener(new ActionListener()
1538 public void actionPerformed(ActionEvent e)
1540 pageSetup_actionPerformed(e);
1543 alignmentProperties.setText("Alignment Properties...");
1544 alignmentProperties.addActionListener(new ActionListener()
1546 public void actionPerformed(ActionEvent actionEvent)
1548 alignmentProperties();
1551 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1552 alignFrameMenuBar.add(fileMenu);
1553 alignFrameMenuBar.add(editMenu);
1554 alignFrameMenuBar.add(selectMenu);
1555 alignFrameMenuBar.add(viewMenu);
1556 alignFrameMenuBar.add(formatMenu);
1557 alignFrameMenuBar.add(colourMenu);
1558 alignFrameMenuBar.add(calculateMenu);
1559 alignFrameMenuBar.add(webService);
1560 fileMenu.add(fetchSequence);
1561 fileMenu.add(addSequenceMenu);
1562 fileMenu.add(reload);
1563 fileMenu.addSeparator();
1564 fileMenu.add(vamsasStore);
1566 fileMenu.add(saveAs);
1567 fileMenu.add(outputTextboxMenu);
1568 fileMenu.add(pageSetup);
1569 fileMenu.add(printMenuItem);
1570 fileMenu.addSeparator();
1571 fileMenu.add(jMenu2);
1572 fileMenu.add(exportFeatures);
1573 fileMenu.add(exportAnnotations);
1574 fileMenu.add(LoadtreeMenuItem);
1575 fileMenu.add(associatedData);
1576 fileMenu.addSeparator();
1577 fileMenu.add(closeMenuItem);
1578 editMenu.add(undoMenuItem);
1579 editMenu.add(redoMenuItem);
1582 editMenu.add(pasteMenu);
1583 editMenu.add(delete);
1584 editMenu.addSeparator();
1585 editMenu.add(remove2LeftMenuItem);
1586 editMenu.add(remove2RightMenuItem);
1587 editMenu.add(removeGappedColumnMenuItem);
1588 editMenu.add(removeAllGapsMenuItem);
1589 editMenu.add(removeRedundancyMenuItem);
1590 editMenu.addSeparator();
1591 // dont add these yet in the CVS build - they cannot be undone!
1592 editMenu.add(justifyLeftMenuItem);
1593 editMenu.add(justifyRightMenuItem);
1594 editMenu.addSeparator();
1595 editMenu.add(padGapsMenuitem);
1596 viewMenu.add(newView);
1597 viewMenu.add(expandViews);
1598 viewMenu.add(gatherViews);
1599 viewMenu.addSeparator();
1600 viewMenu.add(jMenu3);
1601 viewMenu.add(hideMenu);
1602 viewMenu.addSeparator();
1603 viewMenu.add(followHighlightMenuItem);
1604 viewMenu.add(annotationPanelMenuItem);
1605 viewMenu.add(showGroupConservation);
1606 viewMenu.add(showGroupConsensus);
1607 viewMenu.addSeparator();
1608 viewMenu.add(showSeqFeatures);
1609 viewMenu.add(showSeqFeaturesHeight);
1611 viewMenu.add(featureSettings);
1612 tooltipSettingsMenu.add(showDbRefsMenuitem);
1613 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1614 viewMenu.add(tooltipSettingsMenu);
1615 viewMenu.addSeparator();
1616 viewMenu.add(alignmentProperties);
1617 viewMenu.addSeparator();
1618 viewMenu.add(overviewMenuItem);
1619 colourMenu.add(applyToAllGroups);
1620 colourMenu.add(textColour);
1621 colourMenu.addSeparator();
1622 colourMenu.add(noColourmenuItem);
1623 colourMenu.add(clustalColour);
1624 colourMenu.add(BLOSUM62Colour);
1625 colourMenu.add(PIDColour);
1626 colourMenu.add(zappoColour);
1627 colourMenu.add(taylorColour);
1628 colourMenu.add(hydrophobicityColour);
1629 colourMenu.add(helixColour);
1630 colourMenu.add(strandColour);
1631 colourMenu.add(turnColour);
1632 colourMenu.add(buriedColour);
1633 colourMenu.add(nucleotideColour);
1634 colourMenu.add(userDefinedColour);
1635 colourMenu.addSeparator();
1636 colourMenu.add(conservationMenuItem);
1637 colourMenu.add(modifyConservation);
1638 colourMenu.add(abovePIDThreshold);
1639 colourMenu.add(modifyPID);
1640 colourMenu.add(annotationColour);
1641 calculateMenu.add(sort);
1642 calculateMenu.add(calculateTree);
1643 calculateMenu.addSeparator();
1644 calculateMenu.add(pairwiseAlignmentMenuItem);
1645 calculateMenu.add(PCAMenuItem);
1646 calculateMenu.addSeparator();
1647 calculateMenu.add(showTranslation);
1648 calculateMenu.add(showProducts);
1649 calculateMenu.add(autoCalculate);
1650 calculateMenu.addSeparator();
1651 calculateMenu.add(extractScores);
1652 webServiceNoServices = new JMenuItem("<No Services>");
1653 webService.add(webServiceNoServices);
1654 pasteMenu.add(pasteNew);
1655 pasteMenu.add(pasteThis);
1656 sort.add(sortIDMenuItem);
1657 sort.add(sortLengthMenuItem);
1658 sort.add(sortGroupMenuItem);
1659 sort.add(sortPairwiseMenuItem);
1660 sort.add(sortByTreeMenu);
1661 calculateTree.add(averageDistanceTreeMenuItem);
1662 calculateTree.add(neighbourTreeMenuItem);
1663 calculateTree.add(avDistanceTreeBlosumMenuItem);
1664 calculateTree.add(njTreeBlosumMenuItem);
1665 jMenu2.add(htmlMenuItem);
1666 jMenu2.add(epsFile);
1667 jMenu2.add(createPNG);
1668 addSequenceMenu.add(addFromFile);
1669 addSequenceMenu.add(addFromText);
1670 addSequenceMenu.add(addFromURL);
1671 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1672 statusPanel.add(statusBar, null);
1673 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1674 jMenu3.add(showAllColumns);
1675 jMenu3.add(showAllSeqs);
1676 hideMenu.add(hideSelColumns);
1677 hideMenu.add(hideSelSequences);
1678 formatMenu.add(font);
1679 formatMenu.addSeparator();
1680 formatMenu.add(wrapMenuItem);
1681 formatMenu.add(scaleAbove);
1682 formatMenu.add(scaleLeft);
1683 formatMenu.add(scaleRight);
1684 formatMenu.add(seqLimits);
1685 formatMenu.add(idRightAlign);
1686 formatMenu.add(hiddenMarkers);
1687 formatMenu.add(viewBoxesMenuItem);
1688 formatMenu.add(viewTextMenuItem);
1689 formatMenu.add(colourTextMenuItem);
1690 formatMenu.add(renderGapsMenuItem);
1691 formatMenu.add(centreColumnLabelsMenuItem);
1692 formatMenu.add(showUnconservedMenuItem);
1693 selectMenu.add(findMenuItem);
1694 selectMenu.addSeparator();
1695 selectMenu.add(selectAllSequenceMenuItem);
1696 selectMenu.add(deselectAllSequenceMenuItem);
1697 selectMenu.add(invertSequenceMenuItem);
1698 selectMenu.add(invertColSel);
1699 selectMenu.add(deleteGroups);
1702 protected void showGroupConsensus_actionPerformed(ActionEvent e)
1704 // TODO Auto-generated method stub
1708 protected void showGroupConservation_actionPerformed(ActionEvent e)
1710 // TODO Auto-generated method stub
1714 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1716 // TODO Auto-generated method stub
1720 protected void showSeqFeaturesHeight_actionPerformed(
1721 ActionEvent actionEvent)
1723 // TODO Auto-generated method stub
1727 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1729 // TODO Auto-generated method stub
1733 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1735 // TODO Auto-generated method stub
1739 protected void followHighlight_actionPerformed()
1741 // TODO Auto-generated method stub
1745 protected void showNpFeats_actionPerformed(ActionEvent e)
1747 // TODO Auto-generated method stub
1751 protected void showDbRefs_actionPerformed(ActionEvent e)
1753 // TODO Auto-generated method stub
1757 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1761 protected void showProducts_actionPerformed(ActionEvent e)
1765 protected void buildSortByAnnotationScoresMenu()
1769 protected void extractScores_actionPerformed(ActionEvent e)
1773 protected void outputText_actionPerformed(ActionEvent e)
1777 public void addFromFile_actionPerformed(ActionEvent e)
1782 public void addFromText_actionPerformed(ActionEvent e)
1787 public void addFromURL_actionPerformed(ActionEvent e)
1792 public void exportFeatures_actionPerformed(ActionEvent e)
1797 public void exportAnnotations_actionPerformed(ActionEvent e)
1802 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1806 protected void closeMenuItem_actionPerformed(boolean b)
1810 protected void redoMenuItem_actionPerformed(ActionEvent e)
1814 protected void undoMenuItem_actionPerformed(ActionEvent e)
1818 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1822 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1826 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1830 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1834 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1838 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1842 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1846 protected void wrapMenuItem_actionPerformed(ActionEvent e)
1850 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1854 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1858 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1862 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1866 protected void overviewMenuItem_actionPerformed(ActionEvent e)
1870 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1874 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1878 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
1882 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1886 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1890 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1894 protected void PCAMenuItem_actionPerformed(ActionEvent e)
1898 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1902 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1906 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1910 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1914 protected void clustalColour_actionPerformed(ActionEvent e)
1918 protected void zappoColour_actionPerformed(ActionEvent e)
1922 protected void taylorColour_actionPerformed(ActionEvent e)
1926 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1930 protected void helixColour_actionPerformed(ActionEvent e)
1934 protected void strandColour_actionPerformed(ActionEvent e)
1938 protected void turnColour_actionPerformed(ActionEvent e)
1942 protected void buriedColour_actionPerformed(ActionEvent e)
1946 protected void userDefinedColour_actionPerformed(ActionEvent e)
1950 protected void PIDColour_actionPerformed(ActionEvent e)
1954 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1958 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1962 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1966 protected void printMenuItem_actionPerformed(ActionEvent e)
1970 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1974 protected void findMenuItem_actionPerformed(ActionEvent e)
1978 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1982 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
1986 protected void nucleotideColour_actionPerformed(ActionEvent e)
1990 protected void deleteGroups_actionPerformed(ActionEvent e)
1994 protected void copy_actionPerformed(ActionEvent e)
1998 protected void cut_actionPerformed(ActionEvent e)
2002 protected void delete_actionPerformed(ActionEvent e)
2006 protected void pasteNew_actionPerformed(ActionEvent e)
2010 protected void pasteThis_actionPerformed(ActionEvent e)
2014 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2018 public void createPNG(java.io.File f)
2022 protected void font_actionPerformed(ActionEvent e)
2026 protected void seqLimit_actionPerformed(ActionEvent e)
2030 public void seqDBRef_actionPerformed(ActionEvent e)
2035 public void createEPS(java.io.File f)
2039 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2043 protected void jpred_actionPerformed(ActionEvent e)
2047 protected void scaleAbove_actionPerformed(ActionEvent e)
2051 protected void scaleLeft_actionPerformed(ActionEvent e)
2055 protected void scaleRight_actionPerformed(ActionEvent e)
2059 protected void modifyPID_actionPerformed(ActionEvent e)
2063 protected void modifyConservation_actionPerformed(ActionEvent e)
2067 protected void saveAs_actionPerformed(ActionEvent e)
2071 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2075 public void vamsasStore_actionPerformed(ActionEvent e)
2080 public void vamsasLoad_actionPerformed(ActionEvent e)
2085 public void showTranslation_actionPerformed(ActionEvent e)
2090 public void featureSettings_actionPerformed(ActionEvent e)
2095 public void fetchSequence_actionPerformed(ActionEvent e)
2100 public void smoothFont_actionPerformed(ActionEvent e)
2105 public void annotationColour_actionPerformed(ActionEvent e)
2110 public void associatedData_actionPerformed(ActionEvent e)
2115 public void autoCalculate_actionPerformed(ActionEvent e)
2120 public void showAllSeqs_actionPerformed(ActionEvent e)
2125 public void showAllColumns_actionPerformed(ActionEvent e)
2130 public void hideSelSequences_actionPerformed(ActionEvent e)
2135 public void hideSelColumns_actionPerformed(ActionEvent e)
2140 public void hiddenMarkers_actionPerformed(ActionEvent e)
2145 public void findPdbId_actionPerformed(ActionEvent e)
2150 public void enterPdbId_actionPerformed(ActionEvent e)
2155 public void pdbFile_actionPerformed(ActionEvent e)
2160 public void invertColSel_actionPerformed(ActionEvent e)
2165 public void tabSelectionChanged(int sel)
2170 public void tabbedPane_mousePressed(MouseEvent e)
2175 public void tabbedPane_focusGained(FocusEvent e)
2180 public void save_actionPerformed(ActionEvent e)
2185 public void reload_actionPerformed(ActionEvent e)
2190 public void newView_actionPerformed(ActionEvent e)
2195 public void textColour_actionPerformed(ActionEvent e)
2200 public void idRightAlign_actionPerformed(ActionEvent e)
2205 public void expandViews_actionPerformed(ActionEvent e)
2210 public void gatherViews_actionPerformed(ActionEvent e)
2215 public void buildTreeMenu()
2220 public void pageSetup_actionPerformed(ActionEvent e)
2225 public void alignmentProperties()