2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.jbgui;
22 import java.awt.event.*;
25 import javax.swing.event.*;
27 import jalview.schemes.*;
29 public class GAlignFrame extends JInternalFrame
31 protected JMenuBar alignFrameMenuBar = new JMenuBar();
33 protected JMenu fileMenu = new JMenu();
35 protected JMenuItem closeMenuItem = new JMenuItem();
37 protected JMenu editMenu = new JMenu();
39 protected JMenu viewMenu = new JMenu();
41 protected JMenu colourMenu = new JMenu();
43 protected JMenu calculateMenu = new JMenu();
45 protected JMenu webService = new JMenu();
47 protected JMenuItem webServiceNoServices;
49 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
51 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
53 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
55 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
57 protected JMenuItem remove2RightMenuItem = new JMenuItem();
59 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
61 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
63 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
65 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
67 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
69 protected JMenuItem sortIDMenuItem = new JMenuItem();
71 protected JMenuItem 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 JMenuItem htmlMenuItem = new JMenuItem();
127 JMenuItem overviewMenuItem = new JMenuItem();
129 protected JMenuItem undoMenuItem = new JMenuItem();
131 protected JMenuItem redoMenuItem = new JMenuItem();
133 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
135 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
137 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
139 JMenuItem printMenuItem = new JMenuItem();
141 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
143 JMenuItem findMenuItem = new JMenuItem();
145 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
147 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
148 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
150 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
152 JMenuItem deleteGroups = new JMenuItem();
154 JMenuItem delete = new JMenuItem();
156 JMenuItem copy = new JMenuItem();
158 JMenuItem cut = new JMenuItem();
160 JMenu pasteMenu = new JMenu();
162 JMenuItem pasteNew = new JMenuItem();
164 JMenuItem pasteThis = new JMenuItem();
166 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
168 JMenuItem createPNG = new JMenuItem();
170 protected JMenuItem font = new JMenuItem();
172 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
174 JMenuItem epsFile = new JMenuItem();
176 JMenuItem LoadtreeMenuItem = new JMenuItem();
178 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
180 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
182 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
184 protected JMenuItem modifyPID = new JMenuItem();
186 protected JMenuItem modifyConservation = new JMenuItem();
188 protected JMenu sortByTreeMenu = new JMenu();
190 protected JMenu sort = new JMenu();
192 protected JMenu calculateTree = new JMenu();
194 JMenu jMenu2 = new JMenu();
196 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
197 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
198 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
200 protected ButtonGroup colours = new ButtonGroup();
202 JMenuItem vamsasStore = new JMenuItem();
204 protected JMenuItem showTranslation = new JMenuItem();
206 protected JMenuItem extractScores = new JMenuItem();
208 protected JMenu showProducts = new JMenu();
210 public JMenuItem featureSettings = new JMenuItem();
212 JMenuItem fetchSequence = new JMenuItem();
214 JMenuItem annotationColour = new JMenuItem();
216 JMenuItem associatedData = new JMenuItem();
218 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
220 JMenu addSequenceMenu = new JMenu();
222 JMenuItem addFromFile = new JMenuItem();
224 JMenuItem addFromText = new JMenuItem();
226 JMenuItem addFromURL = new JMenuItem();
228 JMenuItem exportAnnotations = new JMenuItem();
230 JMenuItem exportFeatures = new JMenuItem();
232 protected JPanel statusPanel = new JPanel();
234 GridLayout gridLayout1 = new GridLayout();
236 JMenu jMenu3 = new JMenu();
238 JMenuItem showAllSeqs = new JMenuItem();
240 JMenuItem showAllColumns = new JMenuItem();
242 JMenu hideMenu = new JMenu();
244 JMenuItem hideSelSequences = new JMenuItem();
246 JMenuItem hideSelColumns = new JMenuItem();
248 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
250 JMenuItem invertColSel = new JMenuItem();
252 protected JTabbedPane tabbedPane = new JTabbedPane();
254 JMenuItem save = new JMenuItem();
256 protected JMenuItem reload = new JMenuItem();
258 JMenuItem newView = new JMenuItem();
260 JMenuItem textColour = new JMenuItem();
262 JMenu formatMenu = new JMenu();
264 JMenu selectMenu = new JMenu();
266 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
268 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
270 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
272 protected JMenuItem gatherViews = new JMenuItem();
274 protected JMenuItem expandViews = new JMenuItem();
276 JMenuItem pageSetup = new JMenuItem();
278 JMenuItem alignmentProperties = new JMenuItem();
280 JMenu tooltipSettingsMenu = new JMenu();
282 private JMenuItem justifyLeftMenuItem=new JMenuItem();
284 private JMenuItem justifyRightMenuItem=new JMenuItem();
291 setJMenuBar(alignFrameMenuBar);
293 // dynamically fill save as menu with available formats
294 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
296 JMenuItem item = new JMenuItem(
297 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
299 item.addActionListener(new java.awt.event.ActionListener()
301 public void actionPerformed(ActionEvent e)
303 outputText_actionPerformed(e);
307 outputTextboxMenu.add(item);
309 } catch (Exception e)
313 if (!new jalview.util.Platform().isAMac())
315 closeMenuItem.setMnemonic('C');
316 outputTextboxMenu.setMnemonic('T');
317 undoMenuItem.setMnemonic('Z');
318 redoMenuItem.setMnemonic('0');
319 copy.setMnemonic('C');
320 cut.setMnemonic('U');
321 pasteMenu.setMnemonic('P');
322 reload.setMnemonic('R');
325 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
327 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
328 .getUserColourSchemes().keys();
330 while (userColours.hasMoreElements())
332 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
333 userColours.nextElement().toString());
334 radioItem.setName("USER_DEFINED");
335 radioItem.addMouseListener(new MouseAdapter()
337 public void mousePressed(MouseEvent evt)
339 if (evt.isControlDown()
340 || SwingUtilities.isRightMouseButton(evt))
343 .removeActionListener(radioItem.getActionListeners()[0]);
345 int option = JOptionPane.showInternalConfirmDialog(
346 jalview.gui.Desktop.desktop,
347 "Remove from default list?",
348 "Remove user defined colour",
349 JOptionPane.YES_NO_OPTION);
350 if (option == JOptionPane.YES_OPTION)
352 jalview.gui.UserDefinedColours
353 .removeColourFromDefaults(radioItem.getText());
354 colourMenu.remove(radioItem);
358 radioItem.addActionListener(new ActionListener()
360 public void actionPerformed(ActionEvent evt)
362 userDefinedColour_actionPerformed(evt);
369 radioItem.addActionListener(new ActionListener()
371 public void actionPerformed(ActionEvent evt)
373 userDefinedColour_actionPerformed(evt);
376 colourMenu.insert(radioItem, 15);
377 colours.add(radioItem);
380 colours.add(noColourmenuItem);
381 colours.add(clustalColour);
382 colours.add(zappoColour);
383 colours.add(taylorColour);
384 colours.add(hydrophobicityColour);
385 colours.add(helixColour);
386 colours.add(strandColour);
387 colours.add(turnColour);
388 colours.add(buriedColour);
389 colours.add(userDefinedColour);
390 colours.add(PIDColour);
391 colours.add(BLOSUM62Colour);
392 colours.add(nucleotideColour);
394 setColourSelected(jalview.bin.Cache
395 .getDefault("DEFAULT_COLOUR", "None"));
399 public void setColourSelected(String defaultColour)
402 if (defaultColour != null)
404 int index = ColourSchemeProperty
405 .getColourIndexFromName(defaultColour);
409 case ColourSchemeProperty.NONE:
410 noColourmenuItem.setSelected(true);
412 case ColourSchemeProperty.CLUSTAL:
413 clustalColour.setSelected(true);
417 case ColourSchemeProperty.BLOSUM:
418 BLOSUM62Colour.setSelected(true);
422 case ColourSchemeProperty.PID:
423 PIDColour.setSelected(true);
427 case ColourSchemeProperty.ZAPPO:
428 zappoColour.setSelected(true);
432 case ColourSchemeProperty.TAYLOR:
433 taylorColour.setSelected(true);
436 case ColourSchemeProperty.HYDROPHOBIC:
437 hydrophobicityColour.setSelected(true);
441 case ColourSchemeProperty.HELIX:
442 helixColour.setSelected(true);
446 case ColourSchemeProperty.STRAND:
447 strandColour.setSelected(true);
451 case ColourSchemeProperty.TURN:
452 turnColour.setSelected(true);
456 case ColourSchemeProperty.BURIED:
457 buriedColour.setSelected(true);
461 case ColourSchemeProperty.NUCLEOTIDE:
462 nucleotideColour.setSelected(true);
466 case ColourSchemeProperty.USER_DEFINED:
467 userDefinedColour.setSelected(true);
475 private void jbInit() throws Exception
477 fileMenu.setText("File");
478 saveAs.setText("Save As...");
479 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
480 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
481 .getMenuShortcutKeyMask()
482 | java.awt.event.KeyEvent.SHIFT_MASK, false));
483 saveAs.addActionListener(new ActionListener()
485 public void actionPerformed(ActionEvent e)
487 saveAs_actionPerformed(e);
490 closeMenuItem.setText("Close");
491 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
492 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
493 .getMenuShortcutKeyMask(), false));
494 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
496 public void actionPerformed(ActionEvent e)
498 closeMenuItem_actionPerformed(false);
501 editMenu.setText("Edit");
502 viewMenu.setText("View");
503 colourMenu.setText("Colour");
504 calculateMenu.setText("Calculate");
505 webService.setText("Web Service");
506 selectAllSequenceMenuItem.setText("Select All");
507 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
508 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
509 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
510 selectAllSequenceMenuItem
511 .addActionListener(new java.awt.event.ActionListener()
513 public void actionPerformed(ActionEvent e)
515 selectAllSequenceMenuItem_actionPerformed(e);
518 deselectAllSequenceMenuItem.setText("Deselect All");
519 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
520 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
521 deselectAllSequenceMenuItem
522 .addActionListener(new java.awt.event.ActionListener()
524 public void actionPerformed(ActionEvent e)
526 deselectAllSequenceMenuItem_actionPerformed(e);
529 invertSequenceMenuItem.setText("Invert Sequence Selection");
530 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
531 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
532 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
533 invertSequenceMenuItem
534 .addActionListener(new java.awt.event.ActionListener()
536 public void actionPerformed(ActionEvent e)
538 invertSequenceMenuItem_actionPerformed(e);
541 remove2LeftMenuItem.setText("Remove Left");
542 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
543 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
544 .getMenuShortcutKeyMask(), false));
546 .addActionListener(new java.awt.event.ActionListener()
548 public void actionPerformed(ActionEvent e)
550 remove2LeftMenuItem_actionPerformed(e);
553 remove2RightMenuItem.setText("Remove Right");
554 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
555 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
556 .getMenuShortcutKeyMask(), false));
558 .addActionListener(new java.awt.event.ActionListener()
560 public void actionPerformed(ActionEvent e)
562 remove2RightMenuItem_actionPerformed(e);
565 removeGappedColumnMenuItem.setText("Remove Empty Columns");
566 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
567 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
568 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
569 removeGappedColumnMenuItem
570 .addActionListener(new java.awt.event.ActionListener()
572 public void actionPerformed(ActionEvent e)
574 removeGappedColumnMenuItem_actionPerformed(e);
577 removeAllGapsMenuItem.setText("Remove All Gaps");
578 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
579 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
580 .getDefaultToolkit().getMenuShortcutKeyMask()
581 | java.awt.event.KeyEvent.SHIFT_MASK, false));
582 removeAllGapsMenuItem
583 .addActionListener(new java.awt.event.ActionListener()
585 public void actionPerformed(ActionEvent e)
587 removeAllGapsMenuItem_actionPerformed(e);
590 justifyLeftMenuItem.setText("Left Justify Alignment");
591 justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
593 public void actionPerformed(ActionEvent e)
595 justifyLeftMenuItem_actionPerformed(e);
598 justifyRightMenuItem.setText("Right Justify Alignment");
599 justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
601 public void actionPerformed(ActionEvent e)
603 justifyRightMenuItem_actionPerformed(e);
606 viewBoxesMenuItem.setText("Boxes");
607 viewBoxesMenuItem.setState(true);
608 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
610 public void actionPerformed(ActionEvent e)
612 viewBoxesMenuItem_actionPerformed(e);
615 viewTextMenuItem.setText("Text");
616 viewTextMenuItem.setState(true);
617 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
619 public void actionPerformed(ActionEvent e)
621 viewTextMenuItem_actionPerformed(e);
624 sortPairwiseMenuItem.setText("by Pairwise Identity");
626 .addActionListener(new java.awt.event.ActionListener()
628 public void actionPerformed(ActionEvent e)
630 sortPairwiseMenuItem_actionPerformed(e);
633 sortIDMenuItem.setText("by ID");
634 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
636 public void actionPerformed(ActionEvent e)
638 sortIDMenuItem_actionPerformed(e);
641 sortLengthMenuItem.setText("By Length");
642 sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
644 public void actionPerformed(ActionEvent e)
646 sortLengthMenuItem_actionPerformed(e);
649 sortGroupMenuItem.setText("by Group");
650 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
652 public void actionPerformed(ActionEvent e)
654 sortGroupMenuItem_actionPerformed(e);
657 removeRedundancyMenuItem.setText("Remove Redundancy...");
658 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
659 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
660 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
661 removeRedundancyMenuItem
662 .addActionListener(new java.awt.event.ActionListener()
664 public void actionPerformed(ActionEvent e)
666 removeRedundancyMenuItem_actionPerformed(e);
669 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
670 pairwiseAlignmentMenuItem
671 .addActionListener(new java.awt.event.ActionListener()
673 public void actionPerformed(ActionEvent e)
675 pairwiseAlignmentMenuItem_actionPerformed(e);
678 PCAMenuItem.setText("Principal Component Analysis");
679 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
681 public void actionPerformed(ActionEvent e)
683 PCAMenuItem_actionPerformed(e);
686 averageDistanceTreeMenuItem
687 .setText("Average Distance Using % Identity");
688 averageDistanceTreeMenuItem
689 .addActionListener(new java.awt.event.ActionListener()
691 public void actionPerformed(ActionEvent e)
693 averageDistanceTreeMenuItem_actionPerformed(e);
696 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
697 neighbourTreeMenuItem
698 .addActionListener(new java.awt.event.ActionListener()
700 public void actionPerformed(ActionEvent e)
702 neighbourTreeMenuItem_actionPerformed(e);
705 this.getContentPane().setLayout(borderLayout1);
706 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
707 statusBar.setBackground(Color.white);
708 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
709 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
710 statusBar.setText("Status bar");
711 outputTextboxMenu.setText("Output to Textbox");
712 clustalColour.setText("Clustalx");
714 clustalColour.addActionListener(new java.awt.event.ActionListener()
716 public void actionPerformed(ActionEvent e)
718 clustalColour_actionPerformed(e);
721 zappoColour.setText("Zappo");
722 zappoColour.addActionListener(new java.awt.event.ActionListener()
724 public void actionPerformed(ActionEvent e)
726 zappoColour_actionPerformed(e);
729 taylorColour.setText("Taylor");
730 taylorColour.addActionListener(new java.awt.event.ActionListener()
732 public void actionPerformed(ActionEvent e)
734 taylorColour_actionPerformed(e);
737 hydrophobicityColour.setText("Hydrophobicity");
739 .addActionListener(new java.awt.event.ActionListener()
741 public void actionPerformed(ActionEvent e)
743 hydrophobicityColour_actionPerformed(e);
746 helixColour.setText("Helix Propensity");
747 helixColour.addActionListener(new java.awt.event.ActionListener()
749 public void actionPerformed(ActionEvent e)
751 helixColour_actionPerformed(e);
754 strandColour.setText("Strand Propensity");
755 strandColour.addActionListener(new java.awt.event.ActionListener()
757 public void actionPerformed(ActionEvent e)
759 strandColour_actionPerformed(e);
762 turnColour.setText("Turn Propensity");
763 turnColour.addActionListener(new java.awt.event.ActionListener()
765 public void actionPerformed(ActionEvent e)
767 turnColour_actionPerformed(e);
770 buriedColour.setText("Buried Index");
771 buriedColour.addActionListener(new java.awt.event.ActionListener()
773 public void actionPerformed(ActionEvent e)
775 buriedColour_actionPerformed(e);
778 userDefinedColour.setText("User Defined...");
779 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
781 public void actionPerformed(ActionEvent e)
783 userDefinedColour_actionPerformed(e);
786 PIDColour.setText("Percentage Identity");
787 PIDColour.addActionListener(new java.awt.event.ActionListener()
789 public void actionPerformed(ActionEvent e)
791 PIDColour_actionPerformed(e);
794 BLOSUM62Colour.setText("BLOSUM62 Score");
795 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
797 public void actionPerformed(ActionEvent e)
799 BLOSUM62Colour_actionPerformed(e);
802 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
803 avDistanceTreeBlosumMenuItem
804 .addActionListener(new java.awt.event.ActionListener()
806 public void actionPerformed(ActionEvent e)
808 avTreeBlosumMenuItem_actionPerformed(e);
811 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
813 .addActionListener(new java.awt.event.ActionListener()
815 public void actionPerformed(ActionEvent e)
817 njTreeBlosumMenuItem_actionPerformed(e);
820 annotationPanelMenuItem.setActionCommand("");
821 annotationPanelMenuItem.setText("Show Annotations");
822 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
823 "SHOW_ANNOTATIONS", true));
824 annotationPanelMenuItem
825 .addActionListener(new java.awt.event.ActionListener()
827 public void actionPerformed(ActionEvent e)
829 annotationPanelMenuItem_actionPerformed(e);
832 colourTextMenuItem.setText("Colour Text");
834 .addActionListener(new java.awt.event.ActionListener()
836 public void actionPerformed(ActionEvent e)
838 colourTextMenuItem_actionPerformed(e);
841 htmlMenuItem.setText("HTML");
842 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
844 public void actionPerformed(ActionEvent e)
846 htmlMenuItem_actionPerformed(e);
849 overviewMenuItem.setText("Overview Window");
850 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
852 public void actionPerformed(ActionEvent e)
854 overviewMenuItem_actionPerformed(e);
857 undoMenuItem.setEnabled(false);
858 undoMenuItem.setText("Undo");
859 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
860 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
861 .getMenuShortcutKeyMask(), false));
862 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
864 public void actionPerformed(ActionEvent e)
866 undoMenuItem_actionPerformed(e);
869 redoMenuItem.setEnabled(false);
870 redoMenuItem.setText("Redo");
871 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
872 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
873 .getMenuShortcutKeyMask(), false));
874 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
876 public void actionPerformed(ActionEvent e)
878 redoMenuItem_actionPerformed(e);
881 conservationMenuItem.setText("By Conservation");
883 .addActionListener(new java.awt.event.ActionListener()
885 public void actionPerformed(ActionEvent e)
887 conservationMenuItem_actionPerformed(e);
890 noColourmenuItem.setText("None");
891 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
893 public void actionPerformed(ActionEvent e)
895 noColourmenuItem_actionPerformed(e);
898 wrapMenuItem.setText("Wrap");
899 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
901 public void actionPerformed(ActionEvent e)
903 wrapMenuItem_actionPerformed(e);
906 printMenuItem.setText("Print ...");
907 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
908 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
909 .getMenuShortcutKeyMask(), false));
910 printMenuItem.addActionListener(new java.awt.event.ActionListener()
912 public void actionPerformed(ActionEvent e)
914 printMenuItem_actionPerformed(e);
917 renderGapsMenuItem.setText("Show Gaps");
918 renderGapsMenuItem.setState(true);
920 .addActionListener(new java.awt.event.ActionListener()
922 public void actionPerformed(ActionEvent e)
924 renderGapsMenuItem_actionPerformed(e);
927 findMenuItem.setText("Find...");
928 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
929 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
930 .getMenuShortcutKeyMask(), false));
931 findMenuItem.addActionListener(new java.awt.event.ActionListener()
933 public void actionPerformed(ActionEvent e)
935 findMenuItem_actionPerformed(e);
938 abovePIDThreshold.setText("Above Identity Threshold");
939 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
941 public void actionPerformed(ActionEvent e)
943 abovePIDThreshold_actionPerformed(e);
946 showSeqFeatures.setText("Show Sequence Features");
947 showSeqFeatures.addActionListener(new ActionListener()
949 public void actionPerformed(ActionEvent actionEvent)
951 showSeqFeatures_actionPerformed(actionEvent);
954 showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
955 showSeqFeaturesHeight.addActionListener(new ActionListener()
957 public void actionPerformed(ActionEvent actionEvent)
959 showSeqFeaturesHeight_actionPerformed(actionEvent);
962 showDbRefsMenuitem.setText("Show Database Refs");
963 showDbRefsMenuitem.addActionListener(new ActionListener()
966 public void actionPerformed(ActionEvent e)
968 showDbRefs_actionPerformed(e);
972 showNpFeatsMenuitem.setText("Show Non-Positional Features");
973 showNpFeatsMenuitem.addActionListener(new ActionListener()
976 public void actionPerformed(ActionEvent e)
978 showNpFeats_actionPerformed(e);
982 nucleotideColour.setText("Nucleotide");
983 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
985 public void actionPerformed(ActionEvent e)
987 nucleotideColour_actionPerformed(e);
990 deleteGroups.setText("Undefine groups");
991 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
992 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
993 .getMenuShortcutKeyMask(), false));
994 deleteGroups.addActionListener(new java.awt.event.ActionListener()
996 public void actionPerformed(ActionEvent e)
998 deleteGroups_actionPerformed(e);
1001 copy.setText("Copy");
1002 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1003 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1004 .getMenuShortcutKeyMask(), false));
1006 copy.addActionListener(new java.awt.event.ActionListener()
1008 public void actionPerformed(ActionEvent e)
1010 copy_actionPerformed(e);
1014 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1015 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1016 .getMenuShortcutKeyMask(), false));
1017 cut.addActionListener(new java.awt.event.ActionListener()
1019 public void actionPerformed(ActionEvent e)
1021 cut_actionPerformed(e);
1024 delete.setText("Delete");
1025 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1026 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1027 delete.addActionListener(new java.awt.event.ActionListener()
1029 public void actionPerformed(ActionEvent e)
1031 delete_actionPerformed(e);
1034 pasteMenu.setText("Paste");
1035 pasteNew.setText("To New Alignment");
1036 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1037 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1038 .getMenuShortcutKeyMask()
1039 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1040 pasteNew.addActionListener(new java.awt.event.ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 pasteNew_actionPerformed(e);
1047 pasteThis.setText("Add To This Alignment");
1048 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1049 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1050 .getMenuShortcutKeyMask(), false));
1051 pasteThis.addActionListener(new java.awt.event.ActionListener()
1053 public void actionPerformed(ActionEvent e)
1055 pasteThis_actionPerformed(e);
1058 applyToAllGroups.setText("Apply Colour To All Groups");
1059 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1061 public void actionPerformed(ActionEvent e)
1063 applyToAllGroups_actionPerformed(e);
1066 createPNG.addActionListener(new java.awt.event.ActionListener()
1068 public void actionPerformed(ActionEvent e)
1073 createPNG.setActionCommand("Save As PNG Image");
1074 createPNG.setText("PNG");
1075 font.setText("Font...");
1076 font.addActionListener(new java.awt.event.ActionListener()
1078 public void actionPerformed(ActionEvent e)
1080 font_actionPerformed(e);
1084 seqLimits.setText("Show Sequence Limits");
1085 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1086 seqLimits.addActionListener(new java.awt.event.ActionListener()
1088 public void actionPerformed(ActionEvent e)
1090 seqLimit_actionPerformed(e);
1093 epsFile.setText("EPS");
1094 epsFile.addActionListener(new java.awt.event.ActionListener()
1096 public void actionPerformed(ActionEvent e)
1101 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1102 LoadtreeMenuItem.setText("Load Associated Tree");
1103 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1105 public void actionPerformed(ActionEvent e)
1107 LoadtreeMenuItem_actionPerformed(e);
1110 scaleAbove.setVisible(false);
1111 scaleAbove.setText("Scale Above");
1112 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1114 public void actionPerformed(ActionEvent e)
1116 scaleAbove_actionPerformed(e);
1119 scaleLeft.setVisible(false);
1120 scaleLeft.setSelected(true);
1121 scaleLeft.setText("Scale Left");
1122 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 scaleLeft_actionPerformed(e);
1129 scaleRight.setVisible(false);
1130 scaleRight.setSelected(true);
1131 scaleRight.setText("Scale Right");
1132 scaleRight.addActionListener(new java.awt.event.ActionListener()
1134 public void actionPerformed(ActionEvent e)
1136 scaleRight_actionPerformed(e);
1139 centreColumnLabelsMenuItem.setVisible(true);
1140 centreColumnLabelsMenuItem.setState(false);
1141 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1142 centreColumnLabelsMenuItem
1143 .addActionListener(new java.awt.event.ActionListener()
1145 public void actionPerformed(ActionEvent e)
1147 centreColumnLabels_actionPerformed(e);
1150 followHighlightMenuItem.setVisible(true);
1151 followHighlightMenuItem.setState(true);
1152 followHighlightMenuItem.setText("Automatic Scrolling");
1153 followHighlightMenuItem.addActionListener(new ActionListener()
1156 public void actionPerformed(ActionEvent e)
1158 followHighlight_actionPerformed();
1163 modifyPID.setText("Modify Identity Threshold...");
1164 modifyPID.addActionListener(new java.awt.event.ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 modifyPID_actionPerformed(e);
1171 modifyConservation.setText("Modify Conservation Threshold...");
1173 .addActionListener(new java.awt.event.ActionListener()
1175 public void actionPerformed(ActionEvent e)
1177 modifyConservation_actionPerformed(e);
1180 sortByTreeMenu.setText("By Tree Order");
1181 sort.setText("Sort");
1182 sort.addMenuListener(new MenuListener()
1184 public void menuSelected(MenuEvent e)
1189 public void menuDeselected(MenuEvent e)
1193 public void menuCanceled(MenuEvent e)
1197 sortByAnnotScore.setText("by Score");
1198 sort.add(sortByAnnotScore);
1199 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1202 public void menuCanceled(MenuEvent e)
1206 public void menuDeselected(MenuEvent e)
1210 public void menuSelected(MenuEvent e)
1212 buildSortByAnnotationScoresMenu();
1215 sortByAnnotScore.setVisible(false);
1217 calculateTree.setText("Calculate Tree");
1219 jMenu2.setText("Export Image");
1220 padGapsMenuitem.setText("Pad Gaps");
1221 padGapsMenuitem.setState(jalview.bin.Cache
1222 .getDefault("PAD_GAPS", false));
1223 padGapsMenuitem.addActionListener(new ActionListener()
1225 public void actionPerformed(ActionEvent e)
1227 padGapsMenuitem_actionPerformed(e);
1230 vamsasStore.setVisible(false);
1231 vamsasStore.setText("VAMSAS store");
1232 vamsasStore.addActionListener(new ActionListener()
1234 public void actionPerformed(ActionEvent e)
1236 vamsasStore_actionPerformed(e);
1239 showTranslation.setText("Translate cDNA");
1240 showTranslation.addActionListener(new ActionListener()
1242 public void actionPerformed(ActionEvent e)
1244 showTranslation_actionPerformed(e);
1247 extractScores.setText("Extract Scores...");
1248 extractScores.addActionListener(new ActionListener()
1250 public void actionPerformed(ActionEvent e)
1252 extractScores_actionPerformed(e);
1255 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1257 showProducts.setText("Get Cross References");
1259 * showProducts.addActionListener(new ActionListener() {
1261 * public void actionPerformed(ActionEvent e) {
1262 * showProducts_actionPerformed(e); } });
1264 featureSettings.setText("Feature Settings...");
1265 featureSettings.addActionListener(new ActionListener()
1267 public void actionPerformed(ActionEvent e)
1269 featureSettings_actionPerformed(e);
1272 fetchSequence.setText("Fetch Sequence(s)...");
1273 fetchSequence.addActionListener(new ActionListener()
1275 public void actionPerformed(ActionEvent e)
1277 fetchSequence_actionPerformed(e);
1281 annotationColour.setText("By Annotation...");
1282 annotationColour.addActionListener(new ActionListener()
1284 public void actionPerformed(ActionEvent e)
1286 annotationColour_actionPerformed(e);
1289 associatedData.setText("Load Features / Annotations");
1290 associatedData.addActionListener(new ActionListener()
1292 public void actionPerformed(ActionEvent e)
1294 associatedData_actionPerformed(e);
1297 autoCalculate.setText("Autocalculate Consensus");
1298 autoCalculate.setState(jalview.bin.Cache.getDefault(
1299 "AUTO_CALC_CONSENSUS", true));
1300 autoCalculate.addActionListener(new ActionListener()
1302 public void actionPerformed(ActionEvent e)
1304 autoCalculate_actionPerformed(e);
1307 addSequenceMenu.setText("Add Sequences");
1308 addFromFile.setText("From File");
1309 addFromFile.addActionListener(new ActionListener()
1311 public void actionPerformed(ActionEvent e)
1313 addFromFile_actionPerformed(e);
1316 addFromText.setText("From Textbox");
1317 addFromText.addActionListener(new ActionListener()
1319 public void actionPerformed(ActionEvent e)
1321 addFromText_actionPerformed(e);
1324 addFromURL.setText("From URL");
1325 addFromURL.addActionListener(new ActionListener()
1327 public void actionPerformed(ActionEvent e)
1329 addFromURL_actionPerformed(e);
1332 exportFeatures.setText("Export Features...");
1333 exportFeatures.addActionListener(new ActionListener()
1335 public void actionPerformed(ActionEvent e)
1337 exportFeatures_actionPerformed(e);
1340 exportAnnotations.setText("Export Annotations...");
1341 exportAnnotations.addActionListener(new ActionListener()
1343 public void actionPerformed(ActionEvent e)
1345 exportAnnotations_actionPerformed(e);
1348 statusPanel.setLayout(gridLayout1);
1349 jMenu3.setText("Show");
1350 showAllSeqs.setText("All Sequences");
1351 showAllSeqs.addActionListener(new ActionListener()
1353 public void actionPerformed(ActionEvent e)
1355 showAllSeqs_actionPerformed(e);
1358 showAllColumns.setText("All Columns");
1359 showAllColumns.addActionListener(new ActionListener()
1361 public void actionPerformed(ActionEvent e)
1363 showAllColumns_actionPerformed(e);
1366 hideMenu.setText("Hide");
1367 hideSelSequences.setText("Selected Sequences");
1368 hideSelSequences.addActionListener(new ActionListener()
1370 public void actionPerformed(ActionEvent e)
1372 hideSelSequences_actionPerformed(e);
1375 hideSelColumns.setText("Selected Columns");
1376 hideSelColumns.addActionListener(new ActionListener()
1378 public void actionPerformed(ActionEvent e)
1380 hideSelColumns_actionPerformed(e);
1383 hiddenMarkers.setText("Show Hidden Markers");
1384 hiddenMarkers.addActionListener(new ActionListener()
1386 public void actionPerformed(ActionEvent e)
1388 hiddenMarkers_actionPerformed(e);
1391 invertColSel.setText("Invert Column Selection");
1392 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1393 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1394 .getMenuShortcutKeyMask()
1395 | java.awt.event.KeyEvent.ALT_MASK, false));
1396 invertColSel.addActionListener(new ActionListener()
1398 public void actionPerformed(ActionEvent e)
1400 invertColSel_actionPerformed(e);
1403 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1405 public void stateChanged(ChangeEvent evt)
1407 JTabbedPane pane = (JTabbedPane) evt.getSource();
1408 int sel = pane.getSelectedIndex();
1409 tabSelectionChanged(sel);
1412 tabbedPane.addMouseListener(new MouseAdapter()
1414 public void mousePressed(MouseEvent e)
1416 tabbedPane_mousePressed(e);
1419 tabbedPane.addFocusListener(new FocusAdapter()
1421 public void focusGained(FocusEvent e)
1423 tabbedPane_focusGained(e);
1426 save.setText("Save");
1427 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1428 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1429 .getMenuShortcutKeyMask(), false));
1430 save.addActionListener(new ActionListener()
1432 public void actionPerformed(ActionEvent e)
1434 save_actionPerformed(e);
1437 reload.setEnabled(false);
1438 reload.setText("Reload");
1439 reload.addActionListener(new ActionListener()
1441 public void actionPerformed(ActionEvent e)
1443 reload_actionPerformed(e);
1446 newView.setText("New View");
1447 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1448 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1449 .getMenuShortcutKeyMask(), false));
1450 newView.addActionListener(new ActionListener()
1452 public void actionPerformed(ActionEvent e)
1454 newView_actionPerformed(e);
1457 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1458 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1459 textColour.setText("Colour Text ...");
1460 textColour.addActionListener(new ActionListener()
1462 public void actionPerformed(ActionEvent e)
1464 textColour_actionPerformed(e);
1467 formatMenu.setText("Format");
1468 selectMenu.setText("Select");
1469 idRightAlign.setText("Right Align Sequence Id");
1470 idRightAlign.addActionListener(new ActionListener()
1472 public void actionPerformed(ActionEvent e)
1474 idRightAlign_actionPerformed(e);
1477 gatherViews.setEnabled(false);
1478 gatherViews.setText("Gather Views");
1479 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1480 java.awt.event.KeyEvent.VK_G, 0, false));
1481 gatherViews.addActionListener(new ActionListener()
1483 public void actionPerformed(ActionEvent e)
1485 gatherViews_actionPerformed(e);
1488 expandViews.setEnabled(false);
1489 expandViews.setText("Expand Views");
1490 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1491 java.awt.event.KeyEvent.VK_X, 0, false));
1492 expandViews.addActionListener(new ActionListener()
1494 public void actionPerformed(ActionEvent e)
1496 expandViews_actionPerformed(e);
1499 pageSetup.setText("Page Setup ...");
1500 pageSetup.addActionListener(new ActionListener()
1502 public void actionPerformed(ActionEvent e)
1504 pageSetup_actionPerformed(e);
1507 alignmentProperties.setText("Alignment Properties...");
1508 alignmentProperties.addActionListener(new ActionListener()
1510 public void actionPerformed(ActionEvent actionEvent)
1512 alignmentProperties();
1515 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1516 alignFrameMenuBar.add(fileMenu);
1517 alignFrameMenuBar.add(editMenu);
1518 alignFrameMenuBar.add(selectMenu);
1519 alignFrameMenuBar.add(viewMenu);
1520 alignFrameMenuBar.add(formatMenu);
1521 alignFrameMenuBar.add(colourMenu);
1522 alignFrameMenuBar.add(calculateMenu);
1523 alignFrameMenuBar.add(webService);
1524 fileMenu.add(fetchSequence);
1525 fileMenu.add(addSequenceMenu);
1526 fileMenu.add(reload);
1527 fileMenu.addSeparator();
1528 fileMenu.add(vamsasStore);
1530 fileMenu.add(saveAs);
1531 fileMenu.add(outputTextboxMenu);
1532 fileMenu.add(pageSetup);
1533 fileMenu.add(printMenuItem);
1534 fileMenu.addSeparator();
1535 fileMenu.add(jMenu2);
1536 fileMenu.add(exportFeatures);
1537 fileMenu.add(exportAnnotations);
1538 fileMenu.add(LoadtreeMenuItem);
1539 fileMenu.add(associatedData);
1540 fileMenu.addSeparator();
1541 fileMenu.add(closeMenuItem);
1542 editMenu.add(undoMenuItem);
1543 editMenu.add(redoMenuItem);
1546 editMenu.add(pasteMenu);
1547 editMenu.add(delete);
1548 editMenu.addSeparator();
1549 editMenu.add(remove2LeftMenuItem);
1550 editMenu.add(remove2RightMenuItem);
1551 editMenu.add(removeGappedColumnMenuItem);
1552 editMenu.add(removeAllGapsMenuItem);
1553 editMenu.add(removeRedundancyMenuItem);
1554 editMenu.addSeparator();
1555 editMenu.add(justifyLeftMenuItem);
1556 editMenu.add(justifyRightMenuItem);
1557 editMenu.addSeparator();
1558 editMenu.add(padGapsMenuitem);
1559 viewMenu.add(newView);
1560 viewMenu.add(expandViews);
1561 viewMenu.add(gatherViews);
1562 viewMenu.addSeparator();
1563 viewMenu.add(jMenu3);
1564 viewMenu.add(hideMenu);
1565 viewMenu.addSeparator();
1566 viewMenu.add(followHighlightMenuItem);
1567 viewMenu.add(annotationPanelMenuItem);
1568 viewMenu.addSeparator();
1569 viewMenu.add(showSeqFeatures);
1570 viewMenu.add(showSeqFeaturesHeight);
1572 viewMenu.add(featureSettings);
1573 tooltipSettingsMenu.add(showDbRefsMenuitem);
1574 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1575 viewMenu.add(tooltipSettingsMenu);
1576 viewMenu.addSeparator();
1577 viewMenu.add(alignmentProperties);
1578 viewMenu.addSeparator();
1579 viewMenu.add(overviewMenuItem);
1580 colourMenu.add(applyToAllGroups);
1581 colourMenu.add(textColour);
1582 colourMenu.addSeparator();
1583 colourMenu.add(noColourmenuItem);
1584 colourMenu.add(clustalColour);
1585 colourMenu.add(BLOSUM62Colour);
1586 colourMenu.add(PIDColour);
1587 colourMenu.add(zappoColour);
1588 colourMenu.add(taylorColour);
1589 colourMenu.add(hydrophobicityColour);
1590 colourMenu.add(helixColour);
1591 colourMenu.add(strandColour);
1592 colourMenu.add(turnColour);
1593 colourMenu.add(buriedColour);
1594 colourMenu.add(nucleotideColour);
1595 colourMenu.add(userDefinedColour);
1596 colourMenu.addSeparator();
1597 colourMenu.add(conservationMenuItem);
1598 colourMenu.add(modifyConservation);
1599 colourMenu.add(abovePIDThreshold);
1600 colourMenu.add(modifyPID);
1601 colourMenu.add(annotationColour);
1602 calculateMenu.add(sort);
1603 calculateMenu.add(calculateTree);
1604 calculateMenu.addSeparator();
1605 calculateMenu.add(pairwiseAlignmentMenuItem);
1606 calculateMenu.add(PCAMenuItem);
1607 calculateMenu.addSeparator();
1608 calculateMenu.add(showTranslation);
1609 calculateMenu.add(showProducts);
1610 calculateMenu.add(autoCalculate);
1611 calculateMenu.addSeparator();
1612 calculateMenu.add(extractScores);
1613 webServiceNoServices = new JMenuItem("<No Services>");
1614 webService.add(webServiceNoServices);
1615 pasteMenu.add(pasteNew);
1616 pasteMenu.add(pasteThis);
1617 sort.add(sortIDMenuItem);
1618 sort.add(sortLengthMenuItem);
1619 sort.add(sortGroupMenuItem);
1620 sort.add(sortPairwiseMenuItem);
1621 sort.add(sortByTreeMenu);
1622 calculateTree.add(averageDistanceTreeMenuItem);
1623 calculateTree.add(neighbourTreeMenuItem);
1624 calculateTree.add(avDistanceTreeBlosumMenuItem);
1625 calculateTree.add(njTreeBlosumMenuItem);
1626 jMenu2.add(htmlMenuItem);
1627 jMenu2.add(epsFile);
1628 jMenu2.add(createPNG);
1629 addSequenceMenu.add(addFromFile);
1630 addSequenceMenu.add(addFromText);
1631 addSequenceMenu.add(addFromURL);
1632 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1633 statusPanel.add(statusBar, null);
1634 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1635 jMenu3.add(showAllColumns);
1636 jMenu3.add(showAllSeqs);
1637 hideMenu.add(hideSelColumns);
1638 hideMenu.add(hideSelSequences);
1639 formatMenu.add(font);
1640 formatMenu.addSeparator();
1641 formatMenu.add(wrapMenuItem);
1642 formatMenu.add(scaleAbove);
1643 formatMenu.add(scaleLeft);
1644 formatMenu.add(scaleRight);
1645 formatMenu.add(seqLimits);
1646 formatMenu.add(idRightAlign);
1647 formatMenu.add(hiddenMarkers);
1648 formatMenu.add(viewBoxesMenuItem);
1649 formatMenu.add(viewTextMenuItem);
1650 formatMenu.add(colourTextMenuItem);
1651 formatMenu.add(renderGapsMenuItem);
1652 formatMenu.add(centreColumnLabelsMenuItem);
1653 selectMenu.add(findMenuItem);
1654 selectMenu.addSeparator();
1655 selectMenu.add(selectAllSequenceMenuItem);
1656 selectMenu.add(deselectAllSequenceMenuItem);
1657 selectMenu.add(invertSequenceMenuItem);
1658 selectMenu.add(invertColSel);
1659 selectMenu.add(deleteGroups);
1662 protected void showSeqFeaturesHeight_actionPerformed(
1663 ActionEvent actionEvent)
1665 // TODO Auto-generated method stub
1669 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1671 // TODO Auto-generated method stub
1675 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1677 // TODO Auto-generated method stub
1681 protected void followHighlight_actionPerformed()
1683 // TODO Auto-generated method stub
1687 protected void showNpFeats_actionPerformed(ActionEvent e)
1689 // TODO Auto-generated method stub
1693 protected void showDbRefs_actionPerformed(ActionEvent e)
1695 // TODO Auto-generated method stub
1699 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1703 protected void showProducts_actionPerformed(ActionEvent e)
1707 protected void buildSortByAnnotationScoresMenu()
1711 protected void extractScores_actionPerformed(ActionEvent e)
1715 protected void outputText_actionPerformed(ActionEvent e)
1719 public void addFromFile_actionPerformed(ActionEvent e)
1724 public void addFromText_actionPerformed(ActionEvent e)
1729 public void addFromURL_actionPerformed(ActionEvent e)
1734 public void exportFeatures_actionPerformed(ActionEvent e)
1739 public void exportAnnotations_actionPerformed(ActionEvent e)
1744 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1748 protected void closeMenuItem_actionPerformed(boolean b)
1752 protected void redoMenuItem_actionPerformed(ActionEvent e)
1756 protected void undoMenuItem_actionPerformed(ActionEvent e)
1760 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1764 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1768 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1772 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1776 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1780 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1784 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1788 protected void wrapMenuItem_actionPerformed(ActionEvent e)
1792 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1796 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1800 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1804 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1808 protected void overviewMenuItem_actionPerformed(ActionEvent e)
1812 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1816 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1820 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
1824 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1828 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1832 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1836 protected void PCAMenuItem_actionPerformed(ActionEvent e)
1840 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1844 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1848 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1852 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1856 protected void clustalColour_actionPerformed(ActionEvent e)
1860 protected void zappoColour_actionPerformed(ActionEvent e)
1864 protected void taylorColour_actionPerformed(ActionEvent e)
1868 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1872 protected void helixColour_actionPerformed(ActionEvent e)
1876 protected void strandColour_actionPerformed(ActionEvent e)
1880 protected void turnColour_actionPerformed(ActionEvent e)
1884 protected void buriedColour_actionPerformed(ActionEvent e)
1888 protected void userDefinedColour_actionPerformed(ActionEvent e)
1892 protected void PIDColour_actionPerformed(ActionEvent e)
1896 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1900 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1904 protected void conservationMenuItem_actionPerformed(ActionEvent e)
1908 protected void printMenuItem_actionPerformed(ActionEvent e)
1912 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1916 protected void findMenuItem_actionPerformed(ActionEvent e)
1920 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1924 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
1928 protected void nucleotideColour_actionPerformed(ActionEvent e)
1932 protected void deleteGroups_actionPerformed(ActionEvent e)
1936 protected void copy_actionPerformed(ActionEvent e)
1940 protected void cut_actionPerformed(ActionEvent e)
1944 protected void delete_actionPerformed(ActionEvent e)
1948 protected void pasteNew_actionPerformed(ActionEvent e)
1952 protected void pasteThis_actionPerformed(ActionEvent e)
1956 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1960 public void createPNG(java.io.File f)
1964 protected void font_actionPerformed(ActionEvent e)
1968 protected void seqLimit_actionPerformed(ActionEvent e)
1972 public void seqDBRef_actionPerformed(ActionEvent e)
1977 public void createEPS(java.io.File f)
1981 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
1985 protected void jpred_actionPerformed(ActionEvent e)
1989 protected void scaleAbove_actionPerformed(ActionEvent e)
1993 protected void scaleLeft_actionPerformed(ActionEvent e)
1997 protected void scaleRight_actionPerformed(ActionEvent e)
2001 protected void modifyPID_actionPerformed(ActionEvent e)
2005 protected void modifyConservation_actionPerformed(ActionEvent e)
2009 protected void saveAs_actionPerformed(ActionEvent e)
2013 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2017 public void vamsasStore_actionPerformed(ActionEvent e)
2022 public void vamsasLoad_actionPerformed(ActionEvent e)
2027 public void showTranslation_actionPerformed(ActionEvent e)
2032 public void featureSettings_actionPerformed(ActionEvent e)
2037 public void fetchSequence_actionPerformed(ActionEvent e)
2042 public void smoothFont_actionPerformed(ActionEvent e)
2047 public void annotationColour_actionPerformed(ActionEvent e)
2052 public void associatedData_actionPerformed(ActionEvent e)
2057 public void autoCalculate_actionPerformed(ActionEvent e)
2062 public void showAllSeqs_actionPerformed(ActionEvent e)
2067 public void showAllColumns_actionPerformed(ActionEvent e)
2072 public void hideSelSequences_actionPerformed(ActionEvent e)
2077 public void hideSelColumns_actionPerformed(ActionEvent e)
2082 public void hiddenMarkers_actionPerformed(ActionEvent e)
2087 public void findPdbId_actionPerformed(ActionEvent e)
2092 public void enterPdbId_actionPerformed(ActionEvent e)
2097 public void pdbFile_actionPerformed(ActionEvent e)
2102 public void invertColSel_actionPerformed(ActionEvent e)
2107 public void tabSelectionChanged(int sel)
2112 public void tabbedPane_mousePressed(MouseEvent e)
2117 public void tabbedPane_focusGained(FocusEvent e)
2122 public void save_actionPerformed(ActionEvent e)
2127 public void reload_actionPerformed(ActionEvent e)
2132 public void newView_actionPerformed(ActionEvent e)
2137 public void textColour_actionPerformed(ActionEvent e)
2142 public void idRightAlign_actionPerformed(ActionEvent e)
2147 public void expandViews_actionPerformed(ActionEvent e)
2152 public void gatherViews_actionPerformed(ActionEvent e)
2157 public void buildTreeMenu()
2162 public void pageSetup_actionPerformed(ActionEvent e)
2167 public void alignmentProperties()