2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.jbgui;
20 import jalview.schemes.ColourSchemeProperty;
22 import java.awt.BorderLayout;
23 import java.awt.Color;
24 import java.awt.GridLayout;
25 import java.awt.Toolkit;
26 import java.awt.event.ActionEvent;
27 import java.awt.event.ActionListener;
28 import java.awt.event.FocusAdapter;
29 import java.awt.event.FocusEvent;
30 import java.awt.event.MouseAdapter;
31 import java.awt.event.MouseEvent;
33 import javax.swing.BorderFactory;
34 import javax.swing.ButtonGroup;
35 import javax.swing.JCheckBoxMenuItem;
36 import javax.swing.JInternalFrame;
37 import javax.swing.JLabel;
38 import javax.swing.JMenu;
39 import javax.swing.JMenuBar;
40 import javax.swing.JMenuItem;
41 import javax.swing.JOptionPane;
42 import javax.swing.JPanel;
43 import javax.swing.JRadioButtonMenuItem;
44 import javax.swing.JTabbedPane;
45 import javax.swing.SwingUtilities;
46 import javax.swing.event.ChangeEvent;
47 import javax.swing.event.MenuEvent;
48 import javax.swing.event.MenuListener;
50 public class GAlignFrame extends JInternalFrame
52 protected JMenuBar alignFrameMenuBar = new JMenuBar();
54 protected JMenu fileMenu = new JMenu();
56 protected JMenuItem closeMenuItem = new JMenuItem();
58 protected JMenu editMenu = new JMenu();
60 protected JMenu viewMenu = new JMenu();
62 protected JMenu colourMenu = new JMenu();
64 protected JMenu calculateMenu = new JMenu();
66 protected JMenu webService = new JMenu();
68 protected JMenuItem webServiceNoServices;
70 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
72 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
74 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
76 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
78 protected JMenuItem remove2RightMenuItem = new JMenuItem();
80 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
82 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
84 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
86 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
88 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
90 protected JMenuItem sortIDMenuItem = new JMenuItem();
92 protected JMenuItem sortLengthMenuItem = new JMenuItem();
94 protected JMenuItem sortGroupMenuItem = new JMenuItem();
96 protected JMenu sortByAnnotScore = new JMenu();
98 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
100 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
102 protected JMenuItem PCAMenuItem = new JMenuItem();
104 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
106 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
108 BorderLayout borderLayout1 = new BorderLayout();
110 public JLabel statusBar = new JLabel();
112 protected JMenuItem saveAs = new JMenuItem();
114 protected JMenu outputTextboxMenu = new JMenu();
116 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
118 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
120 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
122 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
124 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
126 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
128 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
130 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
132 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
134 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
136 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
138 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
140 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
142 // protected JRadioButtonMenuItem covariationColour = new
143 // JRadioButtonMenuItem();
145 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
148 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
150 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
152 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
154 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
156 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
158 JMenuItem htmlMenuItem = new JMenuItem();
160 JMenuItem overviewMenuItem = new JMenuItem();
162 protected JMenuItem undoMenuItem = new JMenuItem();
164 protected JMenuItem redoMenuItem = new JMenuItem();
166 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
168 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
170 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
172 JMenuItem printMenuItem = new JMenuItem();
174 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
176 JMenuItem findMenuItem = new JMenuItem();
178 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
180 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
182 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
184 JMenuItem deleteGroups = new JMenuItem();
186 JMenuItem delete = new JMenuItem();
188 JMenuItem copy = new JMenuItem();
190 JMenuItem cut = new JMenuItem();
192 JMenu pasteMenu = new JMenu();
194 JMenuItem pasteNew = new JMenuItem();
196 JMenuItem pasteThis = new JMenuItem();
198 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
200 JMenuItem createPNG = new JMenuItem();
202 protected JMenuItem font = new JMenuItem();
204 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
206 JMenuItem epsFile = new JMenuItem();
208 JMenuItem LoadtreeMenuItem = new JMenuItem();
210 JMenuItem loadScoresMenuItem = new JMenuItem();
212 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
214 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
216 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
218 protected JMenuItem modifyPID = new JMenuItem();
220 protected JMenuItem modifyConservation = new JMenuItem();
222 protected JMenu sortByTreeMenu = new JMenu();
224 protected JMenu sort = new JMenu();
226 protected JMenu calculateTree = new JMenu();
228 JMenu jMenu2 = new JMenu();
230 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
232 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
234 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
236 protected ButtonGroup colours = new ButtonGroup();
238 JMenuItem vamsasStore = new JMenuItem();
240 protected JMenuItem showTranslation = new JMenuItem();
242 protected JMenuItem extractScores = new JMenuItem();
244 protected JMenu showProducts = new JMenu();
246 public JMenuItem openFeatureSettings = new JMenuItem();
248 JMenuItem fetchSequence = new JMenuItem();
250 JMenuItem annotationColour = new JMenuItem();
252 protected JMenuItem rnahelicesColour = new JMenuItem();
254 JMenuItem associatedData = new JMenuItem();
256 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
258 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
260 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
262 JMenu addSequenceMenu = new JMenu();
264 JMenuItem addFromFile = new JMenuItem();
266 JMenuItem addFromText = new JMenuItem();
268 JMenuItem addFromURL = new JMenuItem();
270 JMenuItem exportAnnotations = new JMenuItem();
272 JMenuItem exportFeatures = new JMenuItem();
274 protected JPanel statusPanel = new JPanel();
276 GridLayout gridLayout1 = new GridLayout();
278 JMenu jMenu3 = new JMenu();
280 JMenuItem showAllSeqs = new JMenuItem();
282 JMenuItem showAllColumns = new JMenuItem();
284 JMenu hideMenu = new JMenu();
286 JMenuItem hideSelSequences = new JMenuItem();
288 JMenuItem hideSelColumns = new JMenuItem();
290 JMenuItem hideAllButSelection = new JMenuItem();
292 JMenuItem hideAllSelection = new JMenuItem();
294 JMenuItem showAllhidden = new JMenuItem();
296 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
298 JMenuItem invertColSel = new JMenuItem();
300 protected JTabbedPane tabbedPane = new JTabbedPane();
302 JMenuItem save = new JMenuItem();
304 protected JMenuItem reload = new JMenuItem();
306 JMenuItem newView = new JMenuItem();
308 JMenuItem textColour = new JMenuItem();
310 JMenu formatMenu = new JMenu();
312 JMenu selectMenu = new JMenu();
314 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
316 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
318 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
320 protected JMenuItem gatherViews = new JMenuItem();
322 protected JMenuItem expandViews = new JMenuItem();
324 JMenuItem pageSetup = new JMenuItem();
326 JMenuItem alignmentProperties = new JMenuItem();
328 JMenu tooltipSettingsMenu = new JMenu();
330 private JMenuItem justifyLeftMenuItem = new JMenuItem();
332 private JMenuItem justifyRightMenuItem = new JMenuItem();
334 JMenu autoAnnMenu = new JMenu();
336 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
338 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
340 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
342 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
344 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
346 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
348 private JMenuItem grpsFromSelection = new JMenuItem();
355 setJMenuBar(alignFrameMenuBar);
357 // dynamically fill save as menu with available formats
358 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
360 JMenuItem item = new JMenuItem(
361 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
363 item.addActionListener(new java.awt.event.ActionListener()
365 public void actionPerformed(ActionEvent e)
367 outputText_actionPerformed(e);
371 outputTextboxMenu.add(item);
373 } catch (Exception e)
377 if (!new jalview.util.Platform().isAMac())
379 closeMenuItem.setMnemonic('C');
380 outputTextboxMenu.setMnemonic('T');
381 undoMenuItem.setMnemonic('Z');
382 redoMenuItem.setMnemonic('0');
383 copy.setMnemonic('C');
384 cut.setMnemonic('U');
385 pasteMenu.setMnemonic('P');
386 reload.setMnemonic('R');
389 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
391 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
392 .getUserColourSchemes().keys();
394 while (userColours.hasMoreElements())
396 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
397 userColours.nextElement().toString());
398 radioItem.setName("USER_DEFINED");
399 radioItem.addMouseListener(new MouseAdapter()
401 public void mousePressed(MouseEvent evt)
403 if (evt.isControlDown()
404 || SwingUtilities.isRightMouseButton(evt))
406 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
408 int option = JOptionPane.showInternalConfirmDialog(
409 jalview.gui.Desktop.desktop,
410 "Remove from default list?",
411 "Remove user defined colour",
412 JOptionPane.YES_NO_OPTION);
413 if (option == JOptionPane.YES_OPTION)
415 jalview.gui.UserDefinedColours
416 .removeColourFromDefaults(radioItem.getText());
417 colourMenu.remove(radioItem);
421 radioItem.addActionListener(new ActionListener()
423 public void actionPerformed(ActionEvent evt)
425 userDefinedColour_actionPerformed(evt);
432 radioItem.addActionListener(new ActionListener()
434 public void actionPerformed(ActionEvent evt)
436 userDefinedColour_actionPerformed(evt);
439 colourMenu.insert(radioItem, 15);
440 colours.add(radioItem);
443 colours.add(noColourmenuItem);
444 colours.add(clustalColour);
445 colours.add(zappoColour);
446 colours.add(taylorColour);
447 colours.add(hydrophobicityColour);
448 colours.add(helixColour);
449 colours.add(strandColour);
450 colours.add(turnColour);
451 colours.add(buriedColour);
452 colours.add(userDefinedColour);
453 colours.add(PIDColour);
454 colours.add(BLOSUM62Colour);
455 colours.add(nucleotideColour);
456 colours.add(purinePyrimidineColour);
457 // colours.add(covariationColour);
458 colours.add(tcoffeeColour);
460 setColourSelected(jalview.bin.Cache
461 .getDefault("DEFAULT_COLOUR", "None"));
465 public void setColourSelected(String defaultColour)
468 if (defaultColour != null)
470 int index = ColourSchemeProperty
471 .getColourIndexFromName(defaultColour);
475 case ColourSchemeProperty.CLUSTAL:
476 clustalColour.setSelected(true);
480 case ColourSchemeProperty.BLOSUM:
481 BLOSUM62Colour.setSelected(true);
485 case ColourSchemeProperty.PID:
486 PIDColour.setSelected(true);
490 case ColourSchemeProperty.ZAPPO:
491 zappoColour.setSelected(true);
495 case ColourSchemeProperty.TAYLOR:
496 taylorColour.setSelected(true);
499 case ColourSchemeProperty.HYDROPHOBIC:
500 hydrophobicityColour.setSelected(true);
504 case ColourSchemeProperty.HELIX:
505 helixColour.setSelected(true);
509 case ColourSchemeProperty.STRAND:
510 strandColour.setSelected(true);
514 case ColourSchemeProperty.TURN:
515 turnColour.setSelected(true);
519 case ColourSchemeProperty.BURIED:
520 buriedColour.setSelected(true);
524 case ColourSchemeProperty.NUCLEOTIDE:
525 nucleotideColour.setSelected(true);
529 case ColourSchemeProperty.TCOFFEE:
530 tcoffeeColour.setSelected(true);
533 case ColourSchemeProperty.PURINEPYRIMIDINE:
534 purinePyrimidineColour.setSelected(true);
538 * case ColourSchemeProperty.COVARIATION:
539 * covariationColour.setSelected(true);
543 case ColourSchemeProperty.USER_DEFINED:
544 userDefinedColour.setSelected(true);
547 case ColourSchemeProperty.NONE:
549 noColourmenuItem.setSelected(true);
557 private void jbInit() throws Exception
559 fileMenu.setText("File");
560 saveAs.setText("Save As...");
561 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
562 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
563 .getMenuShortcutKeyMask()
564 | java.awt.event.KeyEvent.SHIFT_MASK, false));
565 saveAs.addActionListener(new ActionListener()
567 public void actionPerformed(ActionEvent e)
569 saveAs_actionPerformed(e);
572 closeMenuItem.setText("Close");
573 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
574 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
575 .getMenuShortcutKeyMask(), false));
576 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
578 public void actionPerformed(ActionEvent e)
580 closeMenuItem_actionPerformed(false);
583 editMenu.setText("Edit");
584 viewMenu.setText("View");
585 colourMenu.setText("Colour");
586 calculateMenu.setText("Calculate");
587 webService.setText("Web Service");
588 selectAllSequenceMenuItem.setText("Select All");
589 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
590 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
591 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
592 selectAllSequenceMenuItem
593 .addActionListener(new java.awt.event.ActionListener()
595 public void actionPerformed(ActionEvent e)
597 selectAllSequenceMenuItem_actionPerformed(e);
600 deselectAllSequenceMenuItem.setText("Deselect All");
601 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
602 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
603 deselectAllSequenceMenuItem
604 .addActionListener(new java.awt.event.ActionListener()
606 public void actionPerformed(ActionEvent e)
608 deselectAllSequenceMenuItem_actionPerformed(e);
611 invertSequenceMenuItem.setText("Invert Sequence Selection");
612 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
613 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
614 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
615 invertSequenceMenuItem
616 .addActionListener(new java.awt.event.ActionListener()
618 public void actionPerformed(ActionEvent e)
620 invertSequenceMenuItem_actionPerformed(e);
623 grpsFromSelection.setText("Make Groups for selection");
624 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
626 public void actionPerformed(ActionEvent e)
628 makeGrpsFromSelection_actionPerformed(e);
632 remove2LeftMenuItem.setText("Remove Left");
633 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
634 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
635 .getMenuShortcutKeyMask(), false));
637 .addActionListener(new java.awt.event.ActionListener()
639 public void actionPerformed(ActionEvent e)
641 remove2LeftMenuItem_actionPerformed(e);
644 remove2RightMenuItem.setText("Remove Right");
645 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
646 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
647 .getMenuShortcutKeyMask(), false));
649 .addActionListener(new java.awt.event.ActionListener()
651 public void actionPerformed(ActionEvent e)
653 remove2RightMenuItem_actionPerformed(e);
656 removeGappedColumnMenuItem.setText("Remove Empty Columns");
657 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
658 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
659 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
660 removeGappedColumnMenuItem
661 .addActionListener(new java.awt.event.ActionListener()
663 public void actionPerformed(ActionEvent e)
665 removeGappedColumnMenuItem_actionPerformed(e);
668 removeAllGapsMenuItem.setText("Remove All Gaps");
669 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
670 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
671 .getDefaultToolkit().getMenuShortcutKeyMask()
672 | java.awt.event.KeyEvent.SHIFT_MASK, false));
673 removeAllGapsMenuItem
674 .addActionListener(new java.awt.event.ActionListener()
676 public void actionPerformed(ActionEvent e)
678 removeAllGapsMenuItem_actionPerformed(e);
681 justifyLeftMenuItem.setText("Left Justify Alignment");
683 .addActionListener(new java.awt.event.ActionListener()
685 public void actionPerformed(ActionEvent e)
687 justifyLeftMenuItem_actionPerformed(e);
690 justifyRightMenuItem.setText("Right Justify Alignment");
692 .addActionListener(new java.awt.event.ActionListener()
694 public void actionPerformed(ActionEvent e)
696 justifyRightMenuItem_actionPerformed(e);
699 viewBoxesMenuItem.setText("Boxes");
700 viewBoxesMenuItem.setState(true);
701 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
703 public void actionPerformed(ActionEvent e)
705 viewBoxesMenuItem_actionPerformed(e);
708 viewTextMenuItem.setText("Text");
709 viewTextMenuItem.setState(true);
710 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
712 public void actionPerformed(ActionEvent e)
714 viewTextMenuItem_actionPerformed(e);
717 showNonconservedMenuItem.setText("Show nonconserved");
718 showNonconservedMenuItem.setState(false);
719 showNonconservedMenuItem
720 .addActionListener(new java.awt.event.ActionListener()
722 public void actionPerformed(ActionEvent e)
724 showUnconservedMenuItem_actionPerformed(e);
727 sortPairwiseMenuItem.setText("by Pairwise Identity");
729 .addActionListener(new java.awt.event.ActionListener()
731 public void actionPerformed(ActionEvent e)
733 sortPairwiseMenuItem_actionPerformed(e);
736 sortIDMenuItem.setText("by ID");
737 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
739 public void actionPerformed(ActionEvent e)
741 sortIDMenuItem_actionPerformed(e);
744 sortLengthMenuItem.setText("By Length");
746 .addActionListener(new java.awt.event.ActionListener()
748 public void actionPerformed(ActionEvent e)
750 sortLengthMenuItem_actionPerformed(e);
753 sortGroupMenuItem.setText("by Group");
754 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
756 public void actionPerformed(ActionEvent e)
758 sortGroupMenuItem_actionPerformed(e);
761 removeRedundancyMenuItem.setText("Remove Redundancy...");
762 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
763 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
764 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
765 removeRedundancyMenuItem
766 .addActionListener(new java.awt.event.ActionListener()
768 public void actionPerformed(ActionEvent e)
770 removeRedundancyMenuItem_actionPerformed(e);
773 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
774 pairwiseAlignmentMenuItem
775 .addActionListener(new java.awt.event.ActionListener()
777 public void actionPerformed(ActionEvent e)
779 pairwiseAlignmentMenuItem_actionPerformed(e);
782 PCAMenuItem.setText("Principal Component Analysis");
783 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
785 public void actionPerformed(ActionEvent e)
787 PCAMenuItem_actionPerformed(e);
790 averageDistanceTreeMenuItem
791 .setText("Average Distance Using % Identity");
792 averageDistanceTreeMenuItem
793 .addActionListener(new java.awt.event.ActionListener()
795 public void actionPerformed(ActionEvent e)
797 averageDistanceTreeMenuItem_actionPerformed(e);
800 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
801 neighbourTreeMenuItem
802 .addActionListener(new java.awt.event.ActionListener()
804 public void actionPerformed(ActionEvent e)
806 neighbourTreeMenuItem_actionPerformed(e);
809 this.getContentPane().setLayout(borderLayout1);
810 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
811 statusBar.setBackground(Color.white);
812 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
813 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
814 statusBar.setText("Status bar");
815 outputTextboxMenu.setText("Output to Textbox");
816 clustalColour.setText("Clustalx");
818 clustalColour.addActionListener(new java.awt.event.ActionListener()
820 public void actionPerformed(ActionEvent e)
822 clustalColour_actionPerformed(e);
825 zappoColour.setText("Zappo");
826 zappoColour.addActionListener(new java.awt.event.ActionListener()
828 public void actionPerformed(ActionEvent e)
830 zappoColour_actionPerformed(e);
833 taylorColour.setText("Taylor");
834 taylorColour.addActionListener(new java.awt.event.ActionListener()
836 public void actionPerformed(ActionEvent e)
838 taylorColour_actionPerformed(e);
841 hydrophobicityColour.setText("Hydrophobicity");
843 .addActionListener(new java.awt.event.ActionListener()
845 public void actionPerformed(ActionEvent e)
847 hydrophobicityColour_actionPerformed(e);
850 helixColour.setText("Helix Propensity");
851 helixColour.addActionListener(new java.awt.event.ActionListener()
853 public void actionPerformed(ActionEvent e)
855 helixColour_actionPerformed(e);
858 strandColour.setText("Strand Propensity");
859 strandColour.addActionListener(new java.awt.event.ActionListener()
861 public void actionPerformed(ActionEvent e)
863 strandColour_actionPerformed(e);
866 turnColour.setText("Turn Propensity");
867 turnColour.addActionListener(new java.awt.event.ActionListener()
869 public void actionPerformed(ActionEvent e)
871 turnColour_actionPerformed(e);
874 buriedColour.setText("Buried Index");
875 buriedColour.addActionListener(new java.awt.event.ActionListener()
877 public void actionPerformed(ActionEvent e)
879 buriedColour_actionPerformed(e);
882 userDefinedColour.setText("User Defined...");
883 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
885 public void actionPerformed(ActionEvent e)
887 userDefinedColour_actionPerformed(e);
890 PIDColour.setText("Percentage Identity");
891 PIDColour.addActionListener(new java.awt.event.ActionListener()
893 public void actionPerformed(ActionEvent e)
895 PIDColour_actionPerformed(e);
898 BLOSUM62Colour.setText("BLOSUM62 Score");
899 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
901 public void actionPerformed(ActionEvent e)
903 BLOSUM62Colour_actionPerformed(e);
906 nucleotideColour.setText("Nucleotide");
907 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
909 public void actionPerformed(ActionEvent e)
911 nucleotideColour_actionPerformed(e);
915 purinePyrimidineColour.setText("Purine/Pyrimidine");
916 purinePyrimidineColour
917 .addActionListener(new java.awt.event.ActionListener()
919 public void actionPerformed(ActionEvent e)
921 purinePyrimidineColour_actionPerformed(e);
925 * covariationColour.setText("Covariation");
926 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
927 * public void actionPerformed(ActionEvent e) {
928 * covariationColour_actionPerformed(e); } });
931 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
932 avDistanceTreeBlosumMenuItem
933 .addActionListener(new java.awt.event.ActionListener()
935 public void actionPerformed(ActionEvent e)
937 avTreeBlosumMenuItem_actionPerformed(e);
940 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
942 .addActionListener(new java.awt.event.ActionListener()
944 public void actionPerformed(ActionEvent e)
946 njTreeBlosumMenuItem_actionPerformed(e);
949 annotationPanelMenuItem.setActionCommand("");
950 annotationPanelMenuItem.setText("Show Annotations");
951 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
952 "SHOW_ANNOTATIONS", true));
953 annotationPanelMenuItem
954 .addActionListener(new java.awt.event.ActionListener()
956 public void actionPerformed(ActionEvent e)
958 annotationPanelMenuItem_actionPerformed(e);
961 colourTextMenuItem.setText("Colour Text");
963 .addActionListener(new java.awt.event.ActionListener()
965 public void actionPerformed(ActionEvent e)
967 colourTextMenuItem_actionPerformed(e);
970 htmlMenuItem.setText("HTML");
971 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
973 public void actionPerformed(ActionEvent e)
975 htmlMenuItem_actionPerformed(e);
978 overviewMenuItem.setText("Overview Window");
979 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
981 public void actionPerformed(ActionEvent e)
983 overviewMenuItem_actionPerformed(e);
986 undoMenuItem.setEnabled(false);
987 undoMenuItem.setText("Undo");
988 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
989 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
990 .getMenuShortcutKeyMask(), false));
991 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
993 public void actionPerformed(ActionEvent e)
995 undoMenuItem_actionPerformed(e);
998 redoMenuItem.setEnabled(false);
999 redoMenuItem.setText("Redo");
1000 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1001 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1002 .getMenuShortcutKeyMask(), false));
1003 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 redoMenuItem_actionPerformed(e);
1010 conservationMenuItem.setText("By Conservation");
1011 conservationMenuItem
1012 .addActionListener(new java.awt.event.ActionListener()
1014 public void actionPerformed(ActionEvent e)
1016 conservationMenuItem_actionPerformed(e);
1019 noColourmenuItem.setText("None");
1020 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1022 public void actionPerformed(ActionEvent e)
1024 noColourmenuItem_actionPerformed(e);
1027 wrapMenuItem.setText("Wrap");
1028 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1030 public void actionPerformed(ActionEvent e)
1032 wrapMenuItem_actionPerformed(e);
1035 printMenuItem.setText("Print ...");
1036 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1037 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1038 .getMenuShortcutKeyMask(), false));
1039 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1041 public void actionPerformed(ActionEvent e)
1043 printMenuItem_actionPerformed(e);
1046 renderGapsMenuItem.setText("Show Gaps");
1047 renderGapsMenuItem.setState(true);
1049 .addActionListener(new java.awt.event.ActionListener()
1051 public void actionPerformed(ActionEvent e)
1053 renderGapsMenuItem_actionPerformed(e);
1056 findMenuItem.setText("Find...");
1057 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1058 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1059 .getMenuShortcutKeyMask(), false));
1060 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1062 public void actionPerformed(ActionEvent e)
1064 findMenuItem_actionPerformed(e);
1067 abovePIDThreshold.setText("Above Identity Threshold");
1068 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1070 public void actionPerformed(ActionEvent e)
1072 abovePIDThreshold_actionPerformed(e);
1075 showSeqFeatures.setText("Show Sequence Features");
1076 showSeqFeatures.addActionListener(new ActionListener()
1078 public void actionPerformed(ActionEvent actionEvent)
1080 showSeqFeatures_actionPerformed(actionEvent);
1084 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1085 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1086 * void actionPerformed(ActionEvent actionEvent) {
1087 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1089 showDbRefsMenuitem.setText("Show Database Refs");
1090 showDbRefsMenuitem.addActionListener(new ActionListener()
1093 public void actionPerformed(ActionEvent e)
1095 showDbRefs_actionPerformed(e);
1099 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1100 showNpFeatsMenuitem.addActionListener(new ActionListener()
1103 public void actionPerformed(ActionEvent e)
1105 showNpFeats_actionPerformed(e);
1109 showGroupConservation.setText("Group Conservation");
1110 showGroupConservation.addActionListener(new ActionListener()
1113 public void actionPerformed(ActionEvent e)
1115 showGroupConservation_actionPerformed(e);
1120 showGroupConsensus.setText("Group Consensus");
1121 showGroupConsensus.addActionListener(new ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 showGroupConsensus_actionPerformed(e);
1130 showConsensusHistogram.setText("Show Consensus Histogram");
1131 showConsensusHistogram.addActionListener(new ActionListener()
1134 public void actionPerformed(ActionEvent e)
1136 showConsensusHistogram_actionPerformed(e);
1140 showSequenceLogo.setText("Show Consensus Logo");
1141 showSequenceLogo.addActionListener(new ActionListener()
1144 public void actionPerformed(ActionEvent e)
1146 showSequenceLogo_actionPerformed(e);
1150 normaliseSequenceLogo.setText("Normalise Consensus Logo");
1151 normaliseSequenceLogo.addActionListener(new ActionListener()
1154 public void actionPerformed(ActionEvent e)
1156 normaliseSequenceLogo_actionPerformed(e);
1160 applyAutoAnnotationSettings.setText("Apply to all groups");
1161 applyAutoAnnotationSettings.setState(false);
1162 applyAutoAnnotationSettings.setVisible(true);
1163 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 applyAutoAnnotationSettings_actionPerformed(e);
1173 nucleotideColour.setText("Nucleotide");
1174 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1176 public void actionPerformed(ActionEvent e)
1178 nucleotideColour_actionPerformed(e);
1182 tcoffeeColour.setText("T-Coffee scores");
1183 tcoffeeColour.setEnabled(false);
1184 tcoffeeColour.addActionListener( new ActionListener() {
1187 public void actionPerformed(ActionEvent e) {
1188 tcoffeeColorScheme_actionPerformed(e);
1193 deleteGroups.setText("Undefine groups");
1194 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1195 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1196 .getMenuShortcutKeyMask(), false));
1197 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1199 public void actionPerformed(ActionEvent e)
1201 deleteGroups_actionPerformed(e);
1204 copy.setText("Copy");
1205 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1206 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1207 .getMenuShortcutKeyMask(), false));
1209 copy.addActionListener(new java.awt.event.ActionListener()
1211 public void actionPerformed(ActionEvent e)
1213 copy_actionPerformed(e);
1217 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1218 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1219 .getMenuShortcutKeyMask(), false));
1220 cut.addActionListener(new java.awt.event.ActionListener()
1222 public void actionPerformed(ActionEvent e)
1224 cut_actionPerformed(e);
1227 delete.setText("Delete");
1228 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1229 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1230 delete.addActionListener(new java.awt.event.ActionListener()
1232 public void actionPerformed(ActionEvent e)
1234 delete_actionPerformed(e);
1237 pasteMenu.setText("Paste");
1238 pasteNew.setText("To New Alignment");
1239 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1240 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1241 .getMenuShortcutKeyMask()
1242 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1243 pasteNew.addActionListener(new java.awt.event.ActionListener()
1245 public void actionPerformed(ActionEvent e)
1247 pasteNew_actionPerformed(e);
1250 pasteThis.setText("Add To This Alignment");
1251 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1252 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1253 .getMenuShortcutKeyMask(), false));
1254 pasteThis.addActionListener(new java.awt.event.ActionListener()
1256 public void actionPerformed(ActionEvent e)
1258 pasteThis_actionPerformed(e);
1261 applyToAllGroups.setText("Apply Colour To All Groups");
1262 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1264 public void actionPerformed(ActionEvent e)
1266 applyToAllGroups_actionPerformed(e);
1269 createPNG.addActionListener(new java.awt.event.ActionListener()
1271 public void actionPerformed(ActionEvent e)
1276 createPNG.setActionCommand("Save As PNG Image");
1277 createPNG.setText("PNG");
1278 font.setText("Font...");
1279 font.addActionListener(new java.awt.event.ActionListener()
1281 public void actionPerformed(ActionEvent e)
1283 font_actionPerformed(e);
1287 seqLimits.setText("Show Sequence Limits");
1288 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1289 seqLimits.addActionListener(new java.awt.event.ActionListener()
1291 public void actionPerformed(ActionEvent e)
1293 seqLimit_actionPerformed(e);
1296 epsFile.setText("EPS");
1297 epsFile.addActionListener(new java.awt.event.ActionListener()
1299 public void actionPerformed(ActionEvent e)
1304 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1305 LoadtreeMenuItem.setText("Load Associated Tree");
1306 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1308 public void actionPerformed(ActionEvent e)
1310 LoadtreeMenuItem_actionPerformed(e);
1314 loadScoresMenuItem.setActionCommand("Load T-Coffee scores");
1315 loadScoresMenuItem.setText("Load T-Coffee scores");
1316 loadScoresMenuItem.addActionListener(new ActionListener() {
1319 public void actionPerformed(ActionEvent e) {
1320 loadScores_actionPerformed(e);
1324 scaleAbove.setVisible(false);
1325 scaleAbove.setText("Scale Above");
1326 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1328 public void actionPerformed(ActionEvent e)
1330 scaleAbove_actionPerformed(e);
1333 scaleLeft.setVisible(false);
1334 scaleLeft.setSelected(true);
1335 scaleLeft.setText("Scale Left");
1336 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1338 public void actionPerformed(ActionEvent e)
1340 scaleLeft_actionPerformed(e);
1343 scaleRight.setVisible(false);
1344 scaleRight.setSelected(true);
1345 scaleRight.setText("Scale Right");
1346 scaleRight.addActionListener(new java.awt.event.ActionListener()
1348 public void actionPerformed(ActionEvent e)
1350 scaleRight_actionPerformed(e);
1353 centreColumnLabelsMenuItem.setVisible(true);
1354 centreColumnLabelsMenuItem.setState(false);
1355 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1356 centreColumnLabelsMenuItem
1357 .addActionListener(new java.awt.event.ActionListener()
1359 public void actionPerformed(ActionEvent e)
1361 centreColumnLabels_actionPerformed(e);
1364 followHighlightMenuItem.setVisible(true);
1365 followHighlightMenuItem.setState(true);
1366 followHighlightMenuItem.setText("Automatic Scrolling");
1367 followHighlightMenuItem.addActionListener(new ActionListener()
1370 public void actionPerformed(ActionEvent e)
1372 followHighlight_actionPerformed();
1377 modifyPID.setText("Modify Identity Threshold...");
1378 modifyPID.addActionListener(new java.awt.event.ActionListener()
1380 public void actionPerformed(ActionEvent e)
1382 modifyPID_actionPerformed(e);
1385 modifyConservation.setText("Modify Conservation Threshold...");
1387 .addActionListener(new java.awt.event.ActionListener()
1389 public void actionPerformed(ActionEvent e)
1391 modifyConservation_actionPerformed(e);
1394 sortByTreeMenu.setText("By Tree Order");
1395 sort.setText("Sort");
1396 sort.addMenuListener(new MenuListener()
1398 public void menuSelected(MenuEvent e)
1403 public void menuDeselected(MenuEvent e)
1407 public void menuCanceled(MenuEvent e)
1411 sortByAnnotScore.setText("by Score");
1412 sort.add(sortByAnnotScore);
1413 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1416 public void menuCanceled(MenuEvent e)
1420 public void menuDeselected(MenuEvent e)
1424 public void menuSelected(MenuEvent e)
1426 buildSortByAnnotationScoresMenu();
1429 sortByAnnotScore.setVisible(false);
1431 calculateTree.setText("Calculate Tree");
1433 jMenu2.setText("Export Image");
1434 padGapsMenuitem.setText("Pad Gaps");
1435 padGapsMenuitem.setState(jalview.bin.Cache
1436 .getDefault("PAD_GAPS", false));
1437 padGapsMenuitem.addActionListener(new ActionListener()
1439 public void actionPerformed(ActionEvent e)
1441 padGapsMenuitem_actionPerformed(e);
1444 vamsasStore.setVisible(false);
1445 vamsasStore.setText("VAMSAS store");
1446 vamsasStore.addActionListener(new ActionListener()
1448 public void actionPerformed(ActionEvent e)
1450 vamsasStore_actionPerformed(e);
1453 showTranslation.setText("Translate cDNA");
1454 showTranslation.addActionListener(new ActionListener()
1456 public void actionPerformed(ActionEvent e)
1458 showTranslation_actionPerformed(e);
1461 extractScores.setText("Extract Scores...");
1462 extractScores.addActionListener(new ActionListener()
1464 public void actionPerformed(ActionEvent e)
1466 extractScores_actionPerformed(e);
1469 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1471 showProducts.setText("Get Cross References");
1473 * showProducts.addActionListener(new ActionListener() {
1475 * public void actionPerformed(ActionEvent e) {
1476 * showProducts_actionPerformed(e); } });
1478 openFeatureSettings.setText("Feature Settings...");
1479 openFeatureSettings.addActionListener(new ActionListener()
1481 public void actionPerformed(ActionEvent e)
1483 featureSettings_actionPerformed(e);
1486 fetchSequence.setText("Fetch Sequence(s)...");
1487 fetchSequence.addActionListener(new ActionListener()
1489 public void actionPerformed(ActionEvent e)
1491 fetchSequence_actionPerformed(e);
1495 annotationColour.setText("By Annotation...");
1496 annotationColour.addActionListener(new ActionListener()
1498 public void actionPerformed(ActionEvent e)
1500 annotationColour_actionPerformed(e);
1504 rnahelicesColour.setText("By RNA helices");
1505 rnahelicesColour.addActionListener(new ActionListener()
1507 public void actionPerformed(ActionEvent e)
1509 rnahelicesColour_actionPerformed(e);
1513 associatedData.setText("Load Features / Annotations");
1514 associatedData.addActionListener(new ActionListener()
1516 public void actionPerformed(ActionEvent e)
1518 associatedData_actionPerformed(e);
1521 autoCalculate.setText("Autocalculate Consensus");
1522 autoCalculate.setState(jalview.bin.Cache.getDefault(
1523 "AUTO_CALC_CONSENSUS", true));
1524 autoCalculate.addActionListener(new ActionListener()
1526 public void actionPerformed(ActionEvent e)
1528 autoCalculate_actionPerformed(e);
1531 sortByTree.setText("Sort Alignment With New Tree");
1532 sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1533 sortByTree.setState(jalview.bin.Cache.getDefault(
1534 "SORT_BY_TREE", false));
1535 sortByTree.addActionListener(new ActionListener()
1537 public void actionPerformed(ActionEvent e)
1539 sortByTreeOption_actionPerformed(e);
1543 listenToViewSelections.setText("Listen for selections");
1544 listenToViewSelections.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1545 listenToViewSelections.setState(false);
1546 listenToViewSelections.addActionListener(new ActionListener()
1548 public void actionPerformed(ActionEvent e)
1550 listenToViewSelections_actionPerformed(e);
1554 addSequenceMenu.setText("Add Sequences");
1555 addFromFile.setText("From File");
1556 addFromFile.addActionListener(new ActionListener()
1558 public void actionPerformed(ActionEvent e)
1560 addFromFile_actionPerformed(e);
1563 addFromText.setText("From Textbox");
1564 addFromText.addActionListener(new ActionListener()
1566 public void actionPerformed(ActionEvent e)
1568 addFromText_actionPerformed(e);
1571 addFromURL.setText("From URL");
1572 addFromURL.addActionListener(new ActionListener()
1574 public void actionPerformed(ActionEvent e)
1576 addFromURL_actionPerformed(e);
1579 exportFeatures.setText("Export Features...");
1580 exportFeatures.addActionListener(new ActionListener()
1582 public void actionPerformed(ActionEvent e)
1584 exportFeatures_actionPerformed(e);
1587 exportAnnotations.setText("Export Annotations...");
1588 exportAnnotations.addActionListener(new ActionListener()
1590 public void actionPerformed(ActionEvent e)
1592 exportAnnotations_actionPerformed(e);
1595 statusPanel.setLayout(gridLayout1);
1596 jMenu3.setText("Show");
1597 showAllSeqs.setText("All Sequences");
1598 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1599 showAllSeqs.addActionListener(new ActionListener()
1601 public void actionPerformed(ActionEvent e)
1603 showAllSeqs_actionPerformed(e);
1606 showAllColumns.setText("All Columns");
1607 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1608 showAllColumns.addActionListener(new ActionListener()
1610 public void actionPerformed(ActionEvent e)
1612 showAllColumns_actionPerformed(e);
1615 hideMenu.setText("Hide");
1616 hideSelSequences.setText("Selected Sequences");
1617 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1618 hideSelSequences.addActionListener(new ActionListener()
1620 public void actionPerformed(ActionEvent e)
1622 hideSelSequences_actionPerformed(e);
1625 hideSelColumns.setText("Selected Columns");
1626 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1627 hideSelColumns.addActionListener(new ActionListener()
1629 public void actionPerformed(ActionEvent e)
1631 hideSelColumns_actionPerformed(e);
1634 hideAllSelection.setText("Selected Region");
1635 hideAllSelection.addActionListener(new ActionListener()
1637 public void actionPerformed(ActionEvent e)
1639 hideAllSelection_actionPerformed(e);
1642 // TODO: should be hidden if no selection exists.
1643 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1644 hideAllButSelection.addActionListener(new ActionListener()
1646 public void actionPerformed(ActionEvent e)
1648 hideAllButSelection_actionPerformed(e);
1651 showAllhidden.setText("All Sequences and Columns");
1653 .setToolTipText("H toggles visibility of hidden or selected regions.");
1654 showAllhidden.addActionListener(new ActionListener()
1656 public void actionPerformed(ActionEvent e)
1658 showAllhidden_actionPerformed(e);
1662 hiddenMarkers.setText("Show Hidden Markers");
1663 hiddenMarkers.addActionListener(new ActionListener()
1665 public void actionPerformed(ActionEvent e)
1667 hiddenMarkers_actionPerformed(e);
1670 invertColSel.setText("Invert Column Selection");
1671 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1672 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1673 .getMenuShortcutKeyMask()
1674 | java.awt.event.KeyEvent.ALT_MASK, false));
1675 invertColSel.addActionListener(new ActionListener()
1677 public void actionPerformed(ActionEvent e)
1679 invertColSel_actionPerformed(e);
1682 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1684 public void stateChanged(ChangeEvent evt)
1686 JTabbedPane pane = (JTabbedPane) evt.getSource();
1687 int sel = pane.getSelectedIndex();
1688 tabSelectionChanged(sel);
1691 tabbedPane.addMouseListener(new MouseAdapter()
1693 public void mousePressed(MouseEvent e)
1695 tabbedPane_mousePressed(e);
1698 tabbedPane.addFocusListener(new FocusAdapter()
1700 public void focusGained(FocusEvent e)
1702 tabbedPane_focusGained(e);
1705 save.setText("Save");
1706 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1707 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1708 .getMenuShortcutKeyMask(), false));
1709 save.addActionListener(new ActionListener()
1711 public void actionPerformed(ActionEvent e)
1713 save_actionPerformed(e);
1716 reload.setEnabled(false);
1717 reload.setText("Reload");
1718 reload.addActionListener(new ActionListener()
1720 public void actionPerformed(ActionEvent e)
1722 reload_actionPerformed(e);
1725 newView.setText("New View");
1726 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1727 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1728 .getMenuShortcutKeyMask(), false));
1729 newView.addActionListener(new ActionListener()
1731 public void actionPerformed(ActionEvent e)
1733 newView_actionPerformed(e);
1736 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1737 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1738 textColour.setText("Colour Text ...");
1739 textColour.addActionListener(new ActionListener()
1741 public void actionPerformed(ActionEvent e)
1743 textColour_actionPerformed(e);
1746 formatMenu.setText("Format");
1747 selectMenu.setText("Select");
1748 idRightAlign.setText("Right Align Sequence Id");
1749 idRightAlign.addActionListener(new ActionListener()
1751 public void actionPerformed(ActionEvent e)
1753 idRightAlign_actionPerformed(e);
1756 gatherViews.setEnabled(false);
1757 gatherViews.setText("Gather Views");
1758 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1759 java.awt.event.KeyEvent.VK_G, 0, false));
1760 gatherViews.addActionListener(new ActionListener()
1762 public void actionPerformed(ActionEvent e)
1764 gatherViews_actionPerformed(e);
1767 expandViews.setEnabled(false);
1768 expandViews.setText("Expand Views");
1769 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1770 java.awt.event.KeyEvent.VK_X, 0, false));
1771 expandViews.addActionListener(new ActionListener()
1773 public void actionPerformed(ActionEvent e)
1775 expandViews_actionPerformed(e);
1778 pageSetup.setText("Page Setup ...");
1779 pageSetup.addActionListener(new ActionListener()
1781 public void actionPerformed(ActionEvent e)
1783 pageSetup_actionPerformed(e);
1786 alignmentProperties.setText("Alignment Properties...");
1787 alignmentProperties.addActionListener(new ActionListener()
1789 public void actionPerformed(ActionEvent actionEvent)
1791 alignmentProperties();
1794 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1795 autoAnnMenu.setText("Autocalculated Annotation");
1796 alignFrameMenuBar.add(fileMenu);
1797 alignFrameMenuBar.add(editMenu);
1798 alignFrameMenuBar.add(selectMenu);
1799 alignFrameMenuBar.add(viewMenu);
1800 alignFrameMenuBar.add(formatMenu);
1801 alignFrameMenuBar.add(colourMenu);
1802 alignFrameMenuBar.add(calculateMenu);
1803 alignFrameMenuBar.add(webService);
1804 fileMenu.add(fetchSequence);
1805 fileMenu.add(addSequenceMenu);
1806 fileMenu.add(reload);
1807 fileMenu.addSeparator();
1808 fileMenu.add(vamsasStore);
1810 fileMenu.add(saveAs);
1811 fileMenu.add(outputTextboxMenu);
1812 fileMenu.add(pageSetup);
1813 fileMenu.add(printMenuItem);
1814 fileMenu.addSeparator();
1815 fileMenu.add(jMenu2);
1816 fileMenu.add(exportFeatures);
1817 fileMenu.add(exportAnnotations);
1818 fileMenu.add(LoadtreeMenuItem);
1819 fileMenu.add(associatedData);
1820 fileMenu.add(loadScoresMenuItem);
1821 fileMenu.addSeparator();
1822 fileMenu.add(closeMenuItem);
1823 editMenu.add(undoMenuItem);
1824 editMenu.add(redoMenuItem);
1827 editMenu.add(pasteMenu);
1828 editMenu.add(delete);
1829 editMenu.addSeparator();
1830 editMenu.add(remove2LeftMenuItem);
1831 editMenu.add(remove2RightMenuItem);
1832 editMenu.add(removeGappedColumnMenuItem);
1833 editMenu.add(removeAllGapsMenuItem);
1834 editMenu.add(removeRedundancyMenuItem);
1835 editMenu.addSeparator();
1836 // dont add these yet in the CVS build - they cannot be undone!
1837 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1838 // editMenu.add(justifyLeftMenuItem);
1839 // editMenu.add(justifyRightMenuItem);
1840 // editMenu.addSeparator();
1841 editMenu.add(padGapsMenuitem);
1842 viewMenu.add(newView);
1843 viewMenu.add(expandViews);
1844 viewMenu.add(gatherViews);
1845 viewMenu.addSeparator();
1846 viewMenu.add(jMenu3);
1847 viewMenu.add(hideMenu);
1848 viewMenu.addSeparator();
1849 viewMenu.add(followHighlightMenuItem);
1850 viewMenu.add(annotationPanelMenuItem);
1851 autoAnnMenu.add(applyAutoAnnotationSettings);
1852 autoAnnMenu.add(showConsensusHistogram);
1853 autoAnnMenu.add(showSequenceLogo);
1854 autoAnnMenu.add(normaliseSequenceLogo);
1855 autoAnnMenu.addSeparator();
1856 autoAnnMenu.add(showGroupConservation);
1857 autoAnnMenu.add(showGroupConsensus);
1858 viewMenu.add(autoAnnMenu);
1859 viewMenu.addSeparator();
1860 viewMenu.add(showSeqFeatures);
1861 // viewMenu.add(showSeqFeaturesHeight);
1863 viewMenu.add(openFeatureSettings);
1864 tooltipSettingsMenu.add(showDbRefsMenuitem);
1865 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1866 viewMenu.add(tooltipSettingsMenu);
1867 viewMenu.addSeparator();
1868 viewMenu.add(alignmentProperties);
1869 viewMenu.addSeparator();
1870 viewMenu.add(overviewMenuItem);
1871 colourMenu.add(applyToAllGroups);
1872 colourMenu.add(textColour);
1873 colourMenu.addSeparator();
1874 colourMenu.add(noColourmenuItem);
1875 colourMenu.add(clustalColour);
1876 colourMenu.add(BLOSUM62Colour);
1877 colourMenu.add(PIDColour);
1878 colourMenu.add(zappoColour);
1879 colourMenu.add(taylorColour);
1880 colourMenu.add(hydrophobicityColour);
1881 colourMenu.add(helixColour);
1882 colourMenu.add(strandColour);
1883 colourMenu.add(turnColour);
1884 colourMenu.add(buriedColour);
1885 colourMenu.add(nucleotideColour);
1886 colourMenu.add(purinePyrimidineColour);
1887 // colourMenu.add(covariationColour);
1888 colourMenu.add(tcoffeeColour);
1889 colourMenu.add(userDefinedColour);
1890 colourMenu.addSeparator();
1891 colourMenu.add(conservationMenuItem);
1892 colourMenu.add(modifyConservation);
1893 colourMenu.add(abovePIDThreshold);
1894 colourMenu.add(modifyPID);
1895 colourMenu.add(annotationColour);
1896 colourMenu.add(rnahelicesColour);
1897 calculateMenu.add(sort);
1898 calculateMenu.add(calculateTree);
1899 calculateMenu.addSeparator();
1900 calculateMenu.add(pairwiseAlignmentMenuItem);
1901 calculateMenu.add(PCAMenuItem);
1902 calculateMenu.addSeparator();
1903 calculateMenu.add(showTranslation);
1904 calculateMenu.add(showProducts);
1905 calculateMenu.add(autoCalculate);
1906 calculateMenu.add(sortByTree);
1907 calculateMenu.addSeparator();
1908 calculateMenu.add(extractScores);
1909 webServiceNoServices = new JMenuItem("<No Services>");
1910 webService.add(webServiceNoServices);
1911 pasteMenu.add(pasteNew);
1912 pasteMenu.add(pasteThis);
1913 sort.add(sortIDMenuItem);
1914 sort.add(sortLengthMenuItem);
1915 sort.add(sortGroupMenuItem);
1916 sort.add(sortPairwiseMenuItem);
1917 sort.add(sortByTreeMenu);
1918 calculateTree.add(averageDistanceTreeMenuItem);
1919 calculateTree.add(neighbourTreeMenuItem);
1920 calculateTree.add(avDistanceTreeBlosumMenuItem);
1921 calculateTree.add(njTreeBlosumMenuItem);
1922 jMenu2.add(htmlMenuItem);
1923 jMenu2.add(epsFile);
1924 jMenu2.add(createPNG);
1925 addSequenceMenu.add(addFromFile);
1926 addSequenceMenu.add(addFromText);
1927 addSequenceMenu.add(addFromURL);
1928 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1929 statusPanel.add(statusBar, null);
1930 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1931 jMenu3.add(showAllColumns);
1932 jMenu3.add(showAllSeqs);
1933 jMenu3.add(showAllhidden);
1934 hideMenu.add(hideSelColumns);
1935 hideMenu.add(hideSelSequences);
1936 hideMenu.add(hideAllSelection);
1937 hideMenu.add(hideAllButSelection);
1939 formatMenu.add(font);
1940 formatMenu.addSeparator();
1941 formatMenu.add(wrapMenuItem);
1942 formatMenu.add(scaleAbove);
1943 formatMenu.add(scaleLeft);
1944 formatMenu.add(scaleRight);
1945 formatMenu.add(seqLimits);
1946 formatMenu.add(idRightAlign);
1947 formatMenu.add(hiddenMarkers);
1948 formatMenu.add(viewBoxesMenuItem);
1949 formatMenu.add(viewTextMenuItem);
1950 formatMenu.add(colourTextMenuItem);
1951 formatMenu.add(renderGapsMenuItem);
1952 formatMenu.add(centreColumnLabelsMenuItem);
1953 formatMenu.add(showNonconservedMenuItem);
1954 selectMenu.add(findMenuItem);
1955 selectMenu.addSeparator();
1956 selectMenu.add(selectAllSequenceMenuItem);
1957 selectMenu.add(deselectAllSequenceMenuItem);
1958 selectMenu.add(invertSequenceMenuItem);
1959 selectMenu.add(invertColSel);
1960 selectMenu.add(deleteGroups);
1961 selectMenu.add(grpsFromSelection);
1962 // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
1963 //selectMenu.addSeparator();
1964 //selectMenu.add(listenToViewSelections);
1967 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1969 // TODO Auto-generated method stub
1973 protected void listenToViewSelections_actionPerformed(ActionEvent e)
1975 // TODO Auto-generated method stub
1979 protected void showAllhidden_actionPerformed(ActionEvent e)
1981 // TODO Auto-generated method stub
1985 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1987 // TODO Auto-generated method stub
1991 protected void hideAllSelection_actionPerformed(ActionEvent e)
1993 // TODO Auto-generated method stub
1997 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1999 // TODO Auto-generated method stub
2003 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2005 // TODO Auto-generated method stub
2009 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2011 // TODO Auto-generated method stub
2015 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2017 // TODO Auto-generated method stub
2021 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2023 // TODO Auto-generated method stub
2027 protected void showGroupConservation_actionPerformed(ActionEvent e)
2029 // TODO Auto-generated method stub
2033 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2035 // TODO Auto-generated method stub
2039 protected void showSeqFeaturesHeight_actionPerformed(
2040 ActionEvent actionEvent)
2042 // TODO Auto-generated method stub
2046 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2048 // TODO Auto-generated method stub
2052 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2054 // TODO Auto-generated method stub
2058 protected void followHighlight_actionPerformed()
2060 // TODO Auto-generated method stub
2064 protected void showNpFeats_actionPerformed(ActionEvent e)
2066 // TODO Auto-generated method stub
2070 protected void showDbRefs_actionPerformed(ActionEvent e)
2072 // TODO Auto-generated method stub
2076 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2080 protected void showProducts_actionPerformed(ActionEvent e)
2084 protected void buildSortByAnnotationScoresMenu()
2088 protected void extractScores_actionPerformed(ActionEvent e)
2092 protected void outputText_actionPerformed(ActionEvent e)
2096 public void addFromFile_actionPerformed(ActionEvent e)
2101 public void addFromText_actionPerformed(ActionEvent e)
2106 public void addFromURL_actionPerformed(ActionEvent e)
2111 public void exportFeatures_actionPerformed(ActionEvent e)
2116 public void exportAnnotations_actionPerformed(ActionEvent e)
2121 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2125 protected void closeMenuItem_actionPerformed(boolean b)
2129 protected void redoMenuItem_actionPerformed(ActionEvent e)
2133 protected void undoMenuItem_actionPerformed(ActionEvent e)
2137 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2141 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2145 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2149 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2153 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2157 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2161 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2165 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2169 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2173 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2177 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2181 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2185 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2189 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2193 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2197 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2201 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2205 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2209 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2213 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2217 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2221 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2225 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2229 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2233 protected void clustalColour_actionPerformed(ActionEvent e)
2237 protected void zappoColour_actionPerformed(ActionEvent e)
2241 protected void taylorColour_actionPerformed(ActionEvent e)
2245 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2249 protected void helixColour_actionPerformed(ActionEvent e)
2253 protected void strandColour_actionPerformed(ActionEvent e)
2257 protected void turnColour_actionPerformed(ActionEvent e)
2261 protected void buriedColour_actionPerformed(ActionEvent e)
2265 protected void userDefinedColour_actionPerformed(ActionEvent e)
2269 protected void PIDColour_actionPerformed(ActionEvent e)
2273 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2277 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2282 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2285 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2289 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2293 protected void printMenuItem_actionPerformed(ActionEvent e)
2297 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2301 protected void findMenuItem_actionPerformed(ActionEvent e)
2305 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2309 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2313 protected void nucleotideColour_actionPerformed(ActionEvent e)
2317 protected void deleteGroups_actionPerformed(ActionEvent e)
2321 protected void copy_actionPerformed(ActionEvent e)
2325 protected void cut_actionPerformed(ActionEvent e)
2329 protected void delete_actionPerformed(ActionEvent e)
2333 protected void pasteNew_actionPerformed(ActionEvent e)
2337 protected void pasteThis_actionPerformed(ActionEvent e)
2341 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2345 public void createPNG(java.io.File f)
2349 protected void font_actionPerformed(ActionEvent e)
2353 protected void seqLimit_actionPerformed(ActionEvent e)
2357 public void seqDBRef_actionPerformed(ActionEvent e)
2362 public void createEPS(java.io.File f)
2366 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2372 * Template method to handle the 'load T-Coffee scores' menu event.
2374 * Subclasses override this method to provide a custom action.
2376 * @param event The raised event
2378 protected void loadScores_actionPerformed(ActionEvent event) {
2384 * Template method to handle the 'Color T-Coffee scores' menu event.
2386 * Subclasses override this method to provide a custom action.
2388 * @param event The raised event
2390 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) {
2395 protected void jpred_actionPerformed(ActionEvent e)
2399 protected void scaleAbove_actionPerformed(ActionEvent e)
2403 protected void scaleLeft_actionPerformed(ActionEvent e)
2407 protected void scaleRight_actionPerformed(ActionEvent e)
2411 protected void modifyPID_actionPerformed(ActionEvent e)
2415 protected void modifyConservation_actionPerformed(ActionEvent e)
2419 protected void saveAs_actionPerformed(ActionEvent e)
2423 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2427 public void vamsasStore_actionPerformed(ActionEvent e)
2432 public void vamsasLoad_actionPerformed(ActionEvent e)
2437 public void showTranslation_actionPerformed(ActionEvent e)
2442 public void featureSettings_actionPerformed(ActionEvent e)
2447 public void fetchSequence_actionPerformed(ActionEvent e)
2452 public void smoothFont_actionPerformed(ActionEvent e)
2457 public void annotationColour_actionPerformed(ActionEvent e)
2462 public void rnahelicesColour_actionPerformed(ActionEvent e)
2467 public void associatedData_actionPerformed(ActionEvent e)
2472 public void autoCalculate_actionPerformed(ActionEvent e)
2477 public void sortByTreeOption_actionPerformed(ActionEvent e)
2482 public void showAllSeqs_actionPerformed(ActionEvent e)
2487 public void showAllColumns_actionPerformed(ActionEvent e)
2492 public void hideSelSequences_actionPerformed(ActionEvent e)
2497 public void hideSelColumns_actionPerformed(ActionEvent e)
2502 public void hiddenMarkers_actionPerformed(ActionEvent e)
2507 public void findPdbId_actionPerformed(ActionEvent e)
2512 public void enterPdbId_actionPerformed(ActionEvent e)
2517 public void pdbFile_actionPerformed(ActionEvent e)
2522 public void invertColSel_actionPerformed(ActionEvent e)
2527 public void tabSelectionChanged(int sel)
2532 public void tabbedPane_mousePressed(MouseEvent e)
2537 public void tabbedPane_focusGained(FocusEvent e)
2542 public void save_actionPerformed(ActionEvent e)
2547 public void reload_actionPerformed(ActionEvent e)
2552 public void newView_actionPerformed(ActionEvent e)
2557 public void textColour_actionPerformed(ActionEvent e)
2562 public void idRightAlign_actionPerformed(ActionEvent e)
2567 public void expandViews_actionPerformed(ActionEvent e)
2572 public void gatherViews_actionPerformed(ActionEvent e)
2577 public void buildTreeMenu()
2582 public void pageSetup_actionPerformed(ActionEvent e)
2587 public void alignmentProperties()