2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 RNAInteractionColour = new JRadioButtonMenuItem();
144 // protected JRadioButtonMenuItem covariationColour = new
145 // JRadioButtonMenuItem();
147 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
149 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
151 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
153 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
155 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
157 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
159 JMenuItem htmlMenuItem = new JMenuItem();
161 JMenuItem overviewMenuItem = new JMenuItem();
163 protected JMenuItem undoMenuItem = new JMenuItem();
165 protected JMenuItem redoMenuItem = new JMenuItem();
167 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
169 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
171 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
173 JMenuItem printMenuItem = new JMenuItem();
175 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
177 JMenuItem findMenuItem = new JMenuItem();
179 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
181 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
183 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
185 JMenuItem deleteGroups = new JMenuItem();
187 JMenuItem delete = new JMenuItem();
189 JMenuItem copy = new JMenuItem();
191 JMenuItem cut = new JMenuItem();
193 JMenu pasteMenu = new JMenu();
195 JMenuItem pasteNew = new JMenuItem();
197 JMenuItem pasteThis = new JMenuItem();
199 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
201 JMenuItem createPNG = new JMenuItem();
203 protected JMenuItem font = new JMenuItem();
205 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
207 JMenuItem epsFile = new JMenuItem();
209 JMenuItem LoadtreeMenuItem = new JMenuItem();
211 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
213 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
215 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
217 protected JMenuItem modifyPID = new JMenuItem();
219 protected JMenuItem modifyConservation = new JMenuItem();
221 protected JMenu sortByTreeMenu = new JMenu();
223 protected JMenu sort = new JMenu();
225 protected JMenu calculateTree = new JMenu();
227 JMenu jMenu2 = new JMenu();
229 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
231 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
233 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
235 protected ButtonGroup colours = new ButtonGroup();
237 JMenuItem vamsasStore = new JMenuItem();
239 protected JMenuItem showTranslation = new JMenuItem();
241 protected JMenuItem extractScores = new JMenuItem();
243 protected JMenu showProducts = new JMenu();
245 public JMenuItem openFeatureSettings = new JMenuItem();
247 JMenuItem fetchSequence = new JMenuItem();
249 JMenuItem annotationColour = new JMenuItem();
251 protected JMenuItem rnahelicesColour = new JMenuItem();
253 JMenuItem associatedData = new JMenuItem();
255 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
257 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
259 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
261 JMenu addSequenceMenu = new JMenu();
263 JMenuItem addFromFile = new JMenuItem();
265 JMenuItem addFromText = new JMenuItem();
267 JMenuItem addFromURL = new JMenuItem();
269 JMenuItem exportAnnotations = new JMenuItem();
271 JMenuItem exportFeatures = new JMenuItem();
273 protected JPanel statusPanel = new JPanel();
275 GridLayout gridLayout1 = new GridLayout();
277 JMenu jMenu3 = new JMenu();
279 JMenuItem showAllSeqs = new JMenuItem();
281 JMenuItem showAllColumns = new JMenuItem();
283 JMenu hideMenu = new JMenu();
285 JMenuItem hideSelSequences = new JMenuItem();
287 JMenuItem hideSelColumns = new JMenuItem();
289 JMenuItem hideAllButSelection = new JMenuItem();
291 JMenuItem hideAllSelection = new JMenuItem();
293 JMenuItem showAllhidden = new JMenuItem();
295 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
297 JMenuItem invertColSel = new JMenuItem();
299 protected JTabbedPane tabbedPane = new JTabbedPane();
301 JMenuItem save = new JMenuItem();
303 protected JMenuItem reload = new JMenuItem();
305 JMenuItem newView = new JMenuItem();
307 JMenuItem textColour = new JMenuItem();
309 JMenu formatMenu = new JMenu();
311 JMenu selectMenu = new JMenu();
313 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
315 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
317 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
319 protected JMenuItem gatherViews = new JMenuItem();
321 protected JMenuItem expandViews = new JMenuItem();
323 JMenuItem pageSetup = new JMenuItem();
325 JMenuItem alignmentProperties = new JMenuItem();
327 JMenu tooltipSettingsMenu = new JMenu();
329 private JMenuItem justifyLeftMenuItem = new JMenuItem();
331 private JMenuItem justifyRightMenuItem = new JMenuItem();
333 JMenu autoAnnMenu = new JMenu();
335 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
337 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
339 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
341 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
343 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
345 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
347 private JMenuItem grpsFromSelection = new JMenuItem();
354 setJMenuBar(alignFrameMenuBar);
356 // dynamically fill save as menu with available formats
357 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
359 JMenuItem item = new JMenuItem(
360 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
362 item.addActionListener(new java.awt.event.ActionListener()
364 public void actionPerformed(ActionEvent e)
366 outputText_actionPerformed(e);
370 outputTextboxMenu.add(item);
372 } catch (Exception e)
376 if (!new jalview.util.Platform().isAMac())
378 closeMenuItem.setMnemonic('C');
379 outputTextboxMenu.setMnemonic('T');
380 undoMenuItem.setMnemonic('Z');
381 redoMenuItem.setMnemonic('0');
382 copy.setMnemonic('C');
383 cut.setMnemonic('U');
384 pasteMenu.setMnemonic('P');
385 reload.setMnemonic('R');
388 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
390 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
391 .getUserColourSchemes().keys();
393 while (userColours.hasMoreElements())
395 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
396 userColours.nextElement().toString());
397 radioItem.setName("USER_DEFINED");
398 radioItem.addMouseListener(new MouseAdapter()
400 public void mousePressed(MouseEvent evt)
402 if (evt.isControlDown()
403 || SwingUtilities.isRightMouseButton(evt))
405 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
407 int option = JOptionPane.showInternalConfirmDialog(
408 jalview.gui.Desktop.desktop,
409 "Remove from default list?",
410 "Remove user defined colour",
411 JOptionPane.YES_NO_OPTION);
412 if (option == JOptionPane.YES_OPTION)
414 jalview.gui.UserDefinedColours
415 .removeColourFromDefaults(radioItem.getText());
416 colourMenu.remove(radioItem);
420 radioItem.addActionListener(new ActionListener()
422 public void actionPerformed(ActionEvent evt)
424 userDefinedColour_actionPerformed(evt);
431 radioItem.addActionListener(new ActionListener()
433 public void actionPerformed(ActionEvent evt)
435 userDefinedColour_actionPerformed(evt);
438 colourMenu.insert(radioItem, 15);
439 colours.add(radioItem);
442 colours.add(noColourmenuItem);
443 colours.add(clustalColour);
444 colours.add(zappoColour);
445 colours.add(taylorColour);
446 colours.add(hydrophobicityColour);
447 colours.add(helixColour);
448 colours.add(strandColour);
449 colours.add(turnColour);
450 colours.add(buriedColour);
451 colours.add(userDefinedColour);
452 colours.add(PIDColour);
453 colours.add(BLOSUM62Colour);
454 colours.add(nucleotideColour);
455 colours.add(purinePyrimidineColour);
456 // colours.add(covariationColour);
457 colours.add(tcoffeeColour);
458 colours.add(RNAInteractionColour);
459 setColourSelected(jalview.bin.Cache
460 .getDefault("DEFAULT_COLOUR", "None"));
464 public void setColourSelected(String defaultColour)
467 if (defaultColour != null)
469 int index = ColourSchemeProperty
470 .getColourIndexFromName(defaultColour);
474 case ColourSchemeProperty.CLUSTAL:
475 clustalColour.setSelected(true);
479 case ColourSchemeProperty.BLOSUM:
480 BLOSUM62Colour.setSelected(true);
484 case ColourSchemeProperty.PID:
485 PIDColour.setSelected(true);
489 case ColourSchemeProperty.ZAPPO:
490 zappoColour.setSelected(true);
494 case ColourSchemeProperty.TAYLOR:
495 taylorColour.setSelected(true);
498 case ColourSchemeProperty.HYDROPHOBIC:
499 hydrophobicityColour.setSelected(true);
503 case ColourSchemeProperty.HELIX:
504 helixColour.setSelected(true);
508 case ColourSchemeProperty.STRAND:
509 strandColour.setSelected(true);
513 case ColourSchemeProperty.TURN:
514 turnColour.setSelected(true);
518 case ColourSchemeProperty.BURIED:
519 buriedColour.setSelected(true);
523 case ColourSchemeProperty.NUCLEOTIDE:
524 nucleotideColour.setSelected(true);
528 case ColourSchemeProperty.TCOFFEE:
529 tcoffeeColour.setSelected(true);
532 case ColourSchemeProperty.PURINEPYRIMIDINE:
533 purinePyrimidineColour.setSelected(true);
537 case ColourSchemeProperty.RNAINTERACTION:
538 RNAInteractionColour.setSelected(true);
542 * case ColourSchemeProperty.COVARIATION:
543 * covariationColour.setSelected(true);
547 case ColourSchemeProperty.USER_DEFINED:
548 userDefinedColour.setSelected(true);
551 case ColourSchemeProperty.NONE:
553 noColourmenuItem.setSelected(true);
561 private void jbInit() throws Exception
563 fileMenu.setText("File");
564 saveAs.setText("Save As...");
565 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
566 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
567 .getMenuShortcutKeyMask()
568 | java.awt.event.KeyEvent.SHIFT_MASK, false));
569 saveAs.addActionListener(new ActionListener()
571 public void actionPerformed(ActionEvent e)
573 saveAs_actionPerformed(e);
576 closeMenuItem.setText("Close");
577 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
578 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
579 .getMenuShortcutKeyMask(), false));
580 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
582 public void actionPerformed(ActionEvent e)
584 closeMenuItem_actionPerformed(false);
587 editMenu.setText("Edit");
588 viewMenu.setText("View");
589 colourMenu.setText("Colour");
590 calculateMenu.setText("Calculate");
591 webService.setText("Web Service");
592 selectAllSequenceMenuItem.setText("Select All");
593 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
594 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
595 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
596 selectAllSequenceMenuItem
597 .addActionListener(new java.awt.event.ActionListener()
599 public void actionPerformed(ActionEvent e)
601 selectAllSequenceMenuItem_actionPerformed(e);
604 deselectAllSequenceMenuItem.setText("Deselect All");
605 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
606 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
607 deselectAllSequenceMenuItem
608 .addActionListener(new java.awt.event.ActionListener()
610 public void actionPerformed(ActionEvent e)
612 deselectAllSequenceMenuItem_actionPerformed(e);
615 invertSequenceMenuItem.setText("Invert Sequence Selection");
616 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
617 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
618 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
619 invertSequenceMenuItem
620 .addActionListener(new java.awt.event.ActionListener()
622 public void actionPerformed(ActionEvent e)
624 invertSequenceMenuItem_actionPerformed(e);
627 grpsFromSelection.setText("Make Groups for selection");
628 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
630 public void actionPerformed(ActionEvent e)
632 makeGrpsFromSelection_actionPerformed(e);
636 remove2LeftMenuItem.setText("Remove Left");
637 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
638 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
639 .getMenuShortcutKeyMask(), false));
641 .addActionListener(new java.awt.event.ActionListener()
643 public void actionPerformed(ActionEvent e)
645 remove2LeftMenuItem_actionPerformed(e);
648 remove2RightMenuItem.setText("Remove Right");
649 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
650 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
651 .getMenuShortcutKeyMask(), false));
653 .addActionListener(new java.awt.event.ActionListener()
655 public void actionPerformed(ActionEvent e)
657 remove2RightMenuItem_actionPerformed(e);
660 removeGappedColumnMenuItem.setText("Remove Empty Columns");
661 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
662 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
663 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
664 removeGappedColumnMenuItem
665 .addActionListener(new java.awt.event.ActionListener()
667 public void actionPerformed(ActionEvent e)
669 removeGappedColumnMenuItem_actionPerformed(e);
672 removeAllGapsMenuItem.setText("Remove All Gaps");
673 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
674 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
675 .getDefaultToolkit().getMenuShortcutKeyMask()
676 | java.awt.event.KeyEvent.SHIFT_MASK, false));
677 removeAllGapsMenuItem
678 .addActionListener(new java.awt.event.ActionListener()
680 public void actionPerformed(ActionEvent e)
682 removeAllGapsMenuItem_actionPerformed(e);
685 justifyLeftMenuItem.setText("Left Justify Alignment");
687 .addActionListener(new java.awt.event.ActionListener()
689 public void actionPerformed(ActionEvent e)
691 justifyLeftMenuItem_actionPerformed(e);
694 justifyRightMenuItem.setText("Right Justify Alignment");
696 .addActionListener(new java.awt.event.ActionListener()
698 public void actionPerformed(ActionEvent e)
700 justifyRightMenuItem_actionPerformed(e);
703 viewBoxesMenuItem.setText("Boxes");
704 viewBoxesMenuItem.setState(true);
705 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
707 public void actionPerformed(ActionEvent e)
709 viewBoxesMenuItem_actionPerformed(e);
712 viewTextMenuItem.setText("Text");
713 viewTextMenuItem.setState(true);
714 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
716 public void actionPerformed(ActionEvent e)
718 viewTextMenuItem_actionPerformed(e);
721 showNonconservedMenuItem.setText("Show nonconserved");
722 showNonconservedMenuItem.setState(false);
723 showNonconservedMenuItem
724 .addActionListener(new java.awt.event.ActionListener()
726 public void actionPerformed(ActionEvent e)
728 showUnconservedMenuItem_actionPerformed(e);
731 sortPairwiseMenuItem.setText("by Pairwise Identity");
733 .addActionListener(new java.awt.event.ActionListener()
735 public void actionPerformed(ActionEvent e)
737 sortPairwiseMenuItem_actionPerformed(e);
740 sortIDMenuItem.setText("by ID");
741 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
743 public void actionPerformed(ActionEvent e)
745 sortIDMenuItem_actionPerformed(e);
748 sortLengthMenuItem.setText("By Length");
750 .addActionListener(new java.awt.event.ActionListener()
752 public void actionPerformed(ActionEvent e)
754 sortLengthMenuItem_actionPerformed(e);
757 sortGroupMenuItem.setText("by Group");
758 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
760 public void actionPerformed(ActionEvent e)
762 sortGroupMenuItem_actionPerformed(e);
765 removeRedundancyMenuItem.setText("Remove Redundancy...");
766 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
767 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
768 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
769 removeRedundancyMenuItem
770 .addActionListener(new java.awt.event.ActionListener()
772 public void actionPerformed(ActionEvent e)
774 removeRedundancyMenuItem_actionPerformed(e);
777 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
778 pairwiseAlignmentMenuItem
779 .addActionListener(new java.awt.event.ActionListener()
781 public void actionPerformed(ActionEvent e)
783 pairwiseAlignmentMenuItem_actionPerformed(e);
786 PCAMenuItem.setText("Principal Component Analysis");
787 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
789 public void actionPerformed(ActionEvent e)
791 PCAMenuItem_actionPerformed(e);
794 averageDistanceTreeMenuItem
795 .setText("Average Distance Using % Identity");
796 averageDistanceTreeMenuItem
797 .addActionListener(new java.awt.event.ActionListener()
799 public void actionPerformed(ActionEvent e)
801 averageDistanceTreeMenuItem_actionPerformed(e);
804 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
805 neighbourTreeMenuItem
806 .addActionListener(new java.awt.event.ActionListener()
808 public void actionPerformed(ActionEvent e)
810 neighbourTreeMenuItem_actionPerformed(e);
813 this.getContentPane().setLayout(borderLayout1);
814 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
815 statusBar.setBackground(Color.white);
816 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
817 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
818 statusBar.setText("Status bar");
819 outputTextboxMenu.setText("Output to Textbox");
820 clustalColour.setText("Clustalx");
822 clustalColour.addActionListener(new java.awt.event.ActionListener()
824 public void actionPerformed(ActionEvent e)
826 clustalColour_actionPerformed(e);
829 zappoColour.setText("Zappo");
830 zappoColour.addActionListener(new java.awt.event.ActionListener()
832 public void actionPerformed(ActionEvent e)
834 zappoColour_actionPerformed(e);
837 taylorColour.setText("Taylor");
838 taylorColour.addActionListener(new java.awt.event.ActionListener()
840 public void actionPerformed(ActionEvent e)
842 taylorColour_actionPerformed(e);
845 hydrophobicityColour.setText("Hydrophobicity");
847 .addActionListener(new java.awt.event.ActionListener()
849 public void actionPerformed(ActionEvent e)
851 hydrophobicityColour_actionPerformed(e);
854 helixColour.setText("Helix Propensity");
855 helixColour.addActionListener(new java.awt.event.ActionListener()
857 public void actionPerformed(ActionEvent e)
859 helixColour_actionPerformed(e);
862 strandColour.setText("Strand Propensity");
863 strandColour.addActionListener(new java.awt.event.ActionListener()
865 public void actionPerformed(ActionEvent e)
867 strandColour_actionPerformed(e);
870 turnColour.setText("Turn Propensity");
871 turnColour.addActionListener(new java.awt.event.ActionListener()
873 public void actionPerformed(ActionEvent e)
875 turnColour_actionPerformed(e);
878 buriedColour.setText("Buried Index");
879 buriedColour.addActionListener(new java.awt.event.ActionListener()
881 public void actionPerformed(ActionEvent e)
883 buriedColour_actionPerformed(e);
886 userDefinedColour.setText("User Defined...");
887 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
889 public void actionPerformed(ActionEvent e)
891 userDefinedColour_actionPerformed(e);
894 PIDColour.setText("Percentage Identity");
895 PIDColour.addActionListener(new java.awt.event.ActionListener()
897 public void actionPerformed(ActionEvent e)
899 PIDColour_actionPerformed(e);
902 BLOSUM62Colour.setText("BLOSUM62 Score");
903 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
905 public void actionPerformed(ActionEvent e)
907 BLOSUM62Colour_actionPerformed(e);
910 nucleotideColour.setText("Nucleotide");
911 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
913 public void actionPerformed(ActionEvent e)
915 nucleotideColour_actionPerformed(e);
919 purinePyrimidineColour.setText("Purine/Pyrimidine");
920 purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
922 public void actionPerformed(ActionEvent e)
924 purinePyrimidineColour_actionPerformed(e);
928 RNAInteractionColour.setText("RNA Interaction type");
929 RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
931 public void actionPerformed(ActionEvent e)
933 RNAInteractionColour_actionPerformed(e);
937 * covariationColour.setText("Covariation");
938 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
939 * public void actionPerformed(ActionEvent e) {
940 * covariationColour_actionPerformed(e); } });
943 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
944 avDistanceTreeBlosumMenuItem
945 .addActionListener(new java.awt.event.ActionListener()
947 public void actionPerformed(ActionEvent e)
949 avTreeBlosumMenuItem_actionPerformed(e);
952 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
954 .addActionListener(new java.awt.event.ActionListener()
956 public void actionPerformed(ActionEvent e)
958 njTreeBlosumMenuItem_actionPerformed(e);
961 annotationPanelMenuItem.setActionCommand("");
962 annotationPanelMenuItem.setText("Show Annotations");
963 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
964 "SHOW_ANNOTATIONS", true));
965 annotationPanelMenuItem
966 .addActionListener(new java.awt.event.ActionListener()
968 public void actionPerformed(ActionEvent e)
970 annotationPanelMenuItem_actionPerformed(e);
973 colourTextMenuItem.setText("Colour Text");
975 .addActionListener(new java.awt.event.ActionListener()
977 public void actionPerformed(ActionEvent e)
979 colourTextMenuItem_actionPerformed(e);
982 htmlMenuItem.setText("HTML");
983 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
985 public void actionPerformed(ActionEvent e)
987 htmlMenuItem_actionPerformed(e);
990 overviewMenuItem.setText("Overview Window");
991 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
993 public void actionPerformed(ActionEvent e)
995 overviewMenuItem_actionPerformed(e);
998 undoMenuItem.setEnabled(false);
999 undoMenuItem.setText("Undo");
1000 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1001 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1002 .getMenuShortcutKeyMask(), false));
1003 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 undoMenuItem_actionPerformed(e);
1010 redoMenuItem.setEnabled(false);
1011 redoMenuItem.setText("Redo");
1012 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1013 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1014 .getMenuShortcutKeyMask(), false));
1015 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1017 public void actionPerformed(ActionEvent e)
1019 redoMenuItem_actionPerformed(e);
1022 conservationMenuItem.setText("By Conservation");
1023 conservationMenuItem
1024 .addActionListener(new java.awt.event.ActionListener()
1026 public void actionPerformed(ActionEvent e)
1028 conservationMenuItem_actionPerformed(e);
1031 noColourmenuItem.setText("None");
1032 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1034 public void actionPerformed(ActionEvent e)
1036 noColourmenuItem_actionPerformed(e);
1039 wrapMenuItem.setText("Wrap");
1040 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 wrapMenuItem_actionPerformed(e);
1047 printMenuItem.setText("Print ...");
1048 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1049 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1050 .getMenuShortcutKeyMask(), false));
1051 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1053 public void actionPerformed(ActionEvent e)
1055 printMenuItem_actionPerformed(e);
1058 renderGapsMenuItem.setText("Show Gaps");
1059 renderGapsMenuItem.setState(true);
1061 .addActionListener(new java.awt.event.ActionListener()
1063 public void actionPerformed(ActionEvent e)
1065 renderGapsMenuItem_actionPerformed(e);
1068 findMenuItem.setText("Find...");
1069 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1070 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1071 .getMenuShortcutKeyMask(), false));
1072 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1074 public void actionPerformed(ActionEvent e)
1076 findMenuItem_actionPerformed(e);
1079 abovePIDThreshold.setText("Above Identity Threshold");
1080 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1082 public void actionPerformed(ActionEvent e)
1084 abovePIDThreshold_actionPerformed(e);
1087 showSeqFeatures.setText("Show Sequence Features");
1088 showSeqFeatures.addActionListener(new ActionListener()
1090 public void actionPerformed(ActionEvent actionEvent)
1092 showSeqFeatures_actionPerformed(actionEvent);
1096 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1097 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1098 * void actionPerformed(ActionEvent actionEvent) {
1099 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1101 showDbRefsMenuitem.setText("Show Database Refs");
1102 showDbRefsMenuitem.addActionListener(new ActionListener()
1105 public void actionPerformed(ActionEvent e)
1107 showDbRefs_actionPerformed(e);
1111 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1112 showNpFeatsMenuitem.addActionListener(new ActionListener()
1115 public void actionPerformed(ActionEvent e)
1117 showNpFeats_actionPerformed(e);
1121 showGroupConservation.setText("Group Conservation");
1122 showGroupConservation.addActionListener(new ActionListener()
1125 public void actionPerformed(ActionEvent e)
1127 showGroupConservation_actionPerformed(e);
1132 showGroupConsensus.setText("Group Consensus");
1133 showGroupConsensus.addActionListener(new ActionListener()
1136 public void actionPerformed(ActionEvent e)
1138 showGroupConsensus_actionPerformed(e);
1142 showConsensusHistogram.setText("Show Consensus Histogram");
1143 showConsensusHistogram.addActionListener(new ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 showConsensusHistogram_actionPerformed(e);
1152 showSequenceLogo.setText("Show Consensus Logo");
1153 showSequenceLogo.addActionListener(new ActionListener()
1156 public void actionPerformed(ActionEvent e)
1158 showSequenceLogo_actionPerformed(e);
1162 normaliseSequenceLogo.setText("Normalise Consensus Logo");
1163 normaliseSequenceLogo.addActionListener(new ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 normaliseSequenceLogo_actionPerformed(e);
1172 applyAutoAnnotationSettings.setText("Apply to all groups");
1173 applyAutoAnnotationSettings.setState(false);
1174 applyAutoAnnotationSettings.setVisible(true);
1175 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1178 public void actionPerformed(ActionEvent e)
1180 applyAutoAnnotationSettings_actionPerformed(e);
1185 nucleotideColour.setText("Nucleotide");
1186 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 nucleotideColour_actionPerformed(e);
1194 tcoffeeColour.setText("T-Coffee scores");
1195 tcoffeeColour.setEnabled(false);
1196 tcoffeeColour.addActionListener(new ActionListener()
1200 public void actionPerformed(ActionEvent e)
1202 tcoffeeColorScheme_actionPerformed(e);
1206 deleteGroups.setText("Undefine groups");
1207 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1208 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1209 .getMenuShortcutKeyMask(), false));
1210 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1212 public void actionPerformed(ActionEvent e)
1214 deleteGroups_actionPerformed(e);
1217 copy.setText("Copy");
1218 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1219 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1220 .getMenuShortcutKeyMask(), false));
1222 copy.addActionListener(new java.awt.event.ActionListener()
1224 public void actionPerformed(ActionEvent e)
1226 copy_actionPerformed(e);
1230 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1231 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1232 .getMenuShortcutKeyMask(), false));
1233 cut.addActionListener(new java.awt.event.ActionListener()
1235 public void actionPerformed(ActionEvent e)
1237 cut_actionPerformed(e);
1240 delete.setText("Delete");
1241 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1242 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1243 delete.addActionListener(new java.awt.event.ActionListener()
1245 public void actionPerformed(ActionEvent e)
1247 delete_actionPerformed(e);
1250 pasteMenu.setText("Paste");
1251 pasteNew.setText("To New Alignment");
1252 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1253 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1254 .getMenuShortcutKeyMask()
1255 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1256 pasteNew.addActionListener(new java.awt.event.ActionListener()
1258 public void actionPerformed(ActionEvent e)
1260 pasteNew_actionPerformed(e);
1263 pasteThis.setText("Add To This Alignment");
1264 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1265 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1266 .getMenuShortcutKeyMask(), false));
1267 pasteThis.addActionListener(new java.awt.event.ActionListener()
1269 public void actionPerformed(ActionEvent e)
1271 pasteThis_actionPerformed(e);
1274 applyToAllGroups.setText("Apply Colour To All Groups");
1275 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1277 public void actionPerformed(ActionEvent e)
1279 applyToAllGroups_actionPerformed(e);
1282 createPNG.addActionListener(new java.awt.event.ActionListener()
1284 public void actionPerformed(ActionEvent e)
1289 createPNG.setActionCommand("Save As PNG Image");
1290 createPNG.setText("PNG");
1291 font.setText("Font...");
1292 font.addActionListener(new java.awt.event.ActionListener()
1294 public void actionPerformed(ActionEvent e)
1296 font_actionPerformed(e);
1300 seqLimits.setText("Show Sequence Limits");
1301 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1302 seqLimits.addActionListener(new java.awt.event.ActionListener()
1304 public void actionPerformed(ActionEvent e)
1306 seqLimit_actionPerformed(e);
1309 epsFile.setText("EPS");
1310 epsFile.addActionListener(new java.awt.event.ActionListener()
1312 public void actionPerformed(ActionEvent e)
1317 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1318 LoadtreeMenuItem.setText("Load Associated Tree");
1319 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1321 public void actionPerformed(ActionEvent e)
1323 LoadtreeMenuItem_actionPerformed(e);
1327 scaleAbove.setVisible(false);
1328 scaleAbove.setText("Scale Above");
1329 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1331 public void actionPerformed(ActionEvent e)
1333 scaleAbove_actionPerformed(e);
1336 scaleLeft.setVisible(false);
1337 scaleLeft.setSelected(true);
1338 scaleLeft.setText("Scale Left");
1339 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1341 public void actionPerformed(ActionEvent e)
1343 scaleLeft_actionPerformed(e);
1346 scaleRight.setVisible(false);
1347 scaleRight.setSelected(true);
1348 scaleRight.setText("Scale Right");
1349 scaleRight.addActionListener(new java.awt.event.ActionListener()
1351 public void actionPerformed(ActionEvent e)
1353 scaleRight_actionPerformed(e);
1356 centreColumnLabelsMenuItem.setVisible(true);
1357 centreColumnLabelsMenuItem.setState(false);
1358 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1359 centreColumnLabelsMenuItem
1360 .addActionListener(new java.awt.event.ActionListener()
1362 public void actionPerformed(ActionEvent e)
1364 centreColumnLabels_actionPerformed(e);
1367 followHighlightMenuItem.setVisible(true);
1368 followHighlightMenuItem.setState(true);
1369 followHighlightMenuItem.setText("Automatic Scrolling");
1370 followHighlightMenuItem.addActionListener(new ActionListener()
1373 public void actionPerformed(ActionEvent e)
1375 followHighlight_actionPerformed();
1380 modifyPID.setText("Modify Identity Threshold...");
1381 modifyPID.addActionListener(new java.awt.event.ActionListener()
1383 public void actionPerformed(ActionEvent e)
1385 modifyPID_actionPerformed(e);
1388 modifyConservation.setText("Modify Conservation Threshold...");
1390 .addActionListener(new java.awt.event.ActionListener()
1392 public void actionPerformed(ActionEvent e)
1394 modifyConservation_actionPerformed(e);
1397 sortByTreeMenu.setText("By Tree Order");
1398 sort.setText("Sort");
1399 sort.addMenuListener(new MenuListener()
1401 public void menuSelected(MenuEvent e)
1406 public void menuDeselected(MenuEvent e)
1410 public void menuCanceled(MenuEvent e)
1414 sortByAnnotScore.setText("by Score");
1415 sort.add(sortByAnnotScore);
1416 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1419 public void menuCanceled(MenuEvent e)
1423 public void menuDeselected(MenuEvent e)
1427 public void menuSelected(MenuEvent e)
1429 buildSortByAnnotationScoresMenu();
1432 sortByAnnotScore.setVisible(false);
1434 calculateTree.setText("Calculate Tree");
1436 jMenu2.setText("Export Image");
1437 padGapsMenuitem.setText("Pad Gaps");
1438 padGapsMenuitem.setState(jalview.bin.Cache
1439 .getDefault("PAD_GAPS", false));
1440 padGapsMenuitem.addActionListener(new ActionListener()
1442 public void actionPerformed(ActionEvent e)
1444 padGapsMenuitem_actionPerformed(e);
1447 vamsasStore.setVisible(false);
1448 vamsasStore.setText("VAMSAS store");
1449 vamsasStore.addActionListener(new ActionListener()
1451 public void actionPerformed(ActionEvent e)
1453 vamsasStore_actionPerformed(e);
1456 showTranslation.setText("Translate cDNA");
1457 showTranslation.addActionListener(new ActionListener()
1459 public void actionPerformed(ActionEvent e)
1461 showTranslation_actionPerformed(e);
1464 extractScores.setText("Extract Scores...");
1465 extractScores.addActionListener(new ActionListener()
1467 public void actionPerformed(ActionEvent e)
1469 extractScores_actionPerformed(e);
1472 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1474 showProducts.setText("Get Cross References");
1476 * showProducts.addActionListener(new ActionListener() {
1478 * public void actionPerformed(ActionEvent e) {
1479 * showProducts_actionPerformed(e); } });
1481 openFeatureSettings.setText("Feature Settings...");
1482 openFeatureSettings.addActionListener(new ActionListener()
1484 public void actionPerformed(ActionEvent e)
1486 featureSettings_actionPerformed(e);
1489 fetchSequence.setText("Fetch Sequence(s)...");
1490 fetchSequence.addActionListener(new ActionListener()
1492 public void actionPerformed(ActionEvent e)
1494 fetchSequence_actionPerformed(e);
1498 annotationColour.setText("By Annotation...");
1499 annotationColour.addActionListener(new ActionListener()
1501 public void actionPerformed(ActionEvent e)
1503 annotationColour_actionPerformed(e);
1507 rnahelicesColour.setText("By RNA helices");
1508 rnahelicesColour.addActionListener(new ActionListener()
1510 public void actionPerformed(ActionEvent e)
1512 rnahelicesColour_actionPerformed(e);
1516 associatedData.setText("Load Features / Annotations");
1517 associatedData.addActionListener(new ActionListener()
1519 public void actionPerformed(ActionEvent e)
1521 associatedData_actionPerformed(e);
1524 autoCalculate.setText("Autocalculate Consensus");
1525 autoCalculate.setState(jalview.bin.Cache.getDefault(
1526 "AUTO_CALC_CONSENSUS", true));
1527 autoCalculate.addActionListener(new ActionListener()
1529 public void actionPerformed(ActionEvent e)
1531 autoCalculate_actionPerformed(e);
1534 sortByTree.setText("Sort Alignment With New Tree");
1536 .setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1538 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1539 sortByTree.addActionListener(new ActionListener()
1541 public void actionPerformed(ActionEvent e)
1543 sortByTreeOption_actionPerformed(e);
1547 listenToViewSelections.setText("Listen for selections");
1548 listenToViewSelections
1549 .setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1550 listenToViewSelections.setState(false);
1551 listenToViewSelections.addActionListener(new ActionListener()
1553 public void actionPerformed(ActionEvent e)
1555 listenToViewSelections_actionPerformed(e);
1559 addSequenceMenu.setText("Add Sequences");
1560 addFromFile.setText("From File");
1561 addFromFile.addActionListener(new ActionListener()
1563 public void actionPerformed(ActionEvent e)
1565 addFromFile_actionPerformed(e);
1568 addFromText.setText("From Textbox");
1569 addFromText.addActionListener(new ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 addFromText_actionPerformed(e);
1576 addFromURL.setText("From URL");
1577 addFromURL.addActionListener(new ActionListener()
1579 public void actionPerformed(ActionEvent e)
1581 addFromURL_actionPerformed(e);
1584 exportFeatures.setText("Export Features...");
1585 exportFeatures.addActionListener(new ActionListener()
1587 public void actionPerformed(ActionEvent e)
1589 exportFeatures_actionPerformed(e);
1592 exportAnnotations.setText("Export Annotations...");
1593 exportAnnotations.addActionListener(new ActionListener()
1595 public void actionPerformed(ActionEvent e)
1597 exportAnnotations_actionPerformed(e);
1600 statusPanel.setLayout(gridLayout1);
1601 jMenu3.setText("Show");
1602 showAllSeqs.setText("All Sequences");
1603 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1604 showAllSeqs.addActionListener(new ActionListener()
1606 public void actionPerformed(ActionEvent e)
1608 showAllSeqs_actionPerformed(e);
1611 showAllColumns.setText("All Columns");
1612 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1613 showAllColumns.addActionListener(new ActionListener()
1615 public void actionPerformed(ActionEvent e)
1617 showAllColumns_actionPerformed(e);
1620 hideMenu.setText("Hide");
1621 hideSelSequences.setText("Selected Sequences");
1622 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1623 hideSelSequences.addActionListener(new ActionListener()
1625 public void actionPerformed(ActionEvent e)
1627 hideSelSequences_actionPerformed(e);
1630 hideSelColumns.setText("Selected Columns");
1631 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1632 hideSelColumns.addActionListener(new ActionListener()
1634 public void actionPerformed(ActionEvent e)
1636 hideSelColumns_actionPerformed(e);
1639 hideAllSelection.setText("Selected Region");
1640 hideAllSelection.addActionListener(new ActionListener()
1642 public void actionPerformed(ActionEvent e)
1644 hideAllSelection_actionPerformed(e);
1647 // TODO: should be hidden if no selection exists.
1648 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1649 hideAllButSelection.addActionListener(new ActionListener()
1651 public void actionPerformed(ActionEvent e)
1653 hideAllButSelection_actionPerformed(e);
1656 showAllhidden.setText("All Sequences and Columns");
1658 .setToolTipText("H toggles visibility of hidden or selected regions.");
1659 showAllhidden.addActionListener(new ActionListener()
1661 public void actionPerformed(ActionEvent e)
1663 showAllhidden_actionPerformed(e);
1667 hiddenMarkers.setText("Show Hidden Markers");
1668 hiddenMarkers.addActionListener(new ActionListener()
1670 public void actionPerformed(ActionEvent e)
1672 hiddenMarkers_actionPerformed(e);
1675 invertColSel.setText("Invert Column Selection");
1676 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1677 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1678 .getMenuShortcutKeyMask()
1679 | java.awt.event.KeyEvent.ALT_MASK, false));
1680 invertColSel.addActionListener(new ActionListener()
1682 public void actionPerformed(ActionEvent e)
1684 invertColSel_actionPerformed(e);
1687 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1689 public void stateChanged(ChangeEvent evt)
1691 JTabbedPane pane = (JTabbedPane) evt.getSource();
1692 int sel = pane.getSelectedIndex();
1693 tabSelectionChanged(sel);
1696 tabbedPane.addMouseListener(new MouseAdapter()
1698 public void mousePressed(MouseEvent e)
1700 tabbedPane_mousePressed(e);
1703 tabbedPane.addFocusListener(new FocusAdapter()
1705 public void focusGained(FocusEvent e)
1707 tabbedPane_focusGained(e);
1710 save.setText("Save");
1711 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1712 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1713 .getMenuShortcutKeyMask(), false));
1714 save.addActionListener(new ActionListener()
1716 public void actionPerformed(ActionEvent e)
1718 save_actionPerformed(e);
1721 reload.setEnabled(false);
1722 reload.setText("Reload");
1723 reload.addActionListener(new ActionListener()
1725 public void actionPerformed(ActionEvent e)
1727 reload_actionPerformed(e);
1730 newView.setText("New View");
1731 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1732 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1733 .getMenuShortcutKeyMask(), false));
1734 newView.addActionListener(new ActionListener()
1736 public void actionPerformed(ActionEvent e)
1738 newView_actionPerformed(e);
1741 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1742 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1743 textColour.setText("Colour Text ...");
1744 textColour.addActionListener(new ActionListener()
1746 public void actionPerformed(ActionEvent e)
1748 textColour_actionPerformed(e);
1751 formatMenu.setText("Format");
1752 selectMenu.setText("Select");
1753 idRightAlign.setText("Right Align Sequence Id");
1754 idRightAlign.addActionListener(new ActionListener()
1756 public void actionPerformed(ActionEvent e)
1758 idRightAlign_actionPerformed(e);
1761 gatherViews.setEnabled(false);
1762 gatherViews.setText("Gather Views");
1763 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1764 java.awt.event.KeyEvent.VK_G, 0, false));
1765 gatherViews.addActionListener(new ActionListener()
1767 public void actionPerformed(ActionEvent e)
1769 gatherViews_actionPerformed(e);
1772 expandViews.setEnabled(false);
1773 expandViews.setText("Expand Views");
1774 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1775 java.awt.event.KeyEvent.VK_X, 0, false));
1776 expandViews.addActionListener(new ActionListener()
1778 public void actionPerformed(ActionEvent e)
1780 expandViews_actionPerformed(e);
1783 pageSetup.setText("Page Setup ...");
1784 pageSetup.addActionListener(new ActionListener()
1786 public void actionPerformed(ActionEvent e)
1788 pageSetup_actionPerformed(e);
1791 alignmentProperties.setText("Alignment Properties...");
1792 alignmentProperties.addActionListener(new ActionListener()
1794 public void actionPerformed(ActionEvent actionEvent)
1796 alignmentProperties();
1799 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1800 autoAnnMenu.setText("Autocalculated Annotation");
1801 alignFrameMenuBar.add(fileMenu);
1802 alignFrameMenuBar.add(editMenu);
1803 alignFrameMenuBar.add(selectMenu);
1804 alignFrameMenuBar.add(viewMenu);
1805 alignFrameMenuBar.add(formatMenu);
1806 alignFrameMenuBar.add(colourMenu);
1807 alignFrameMenuBar.add(calculateMenu);
1808 alignFrameMenuBar.add(webService);
1809 fileMenu.add(fetchSequence);
1810 fileMenu.add(addSequenceMenu);
1811 fileMenu.add(reload);
1812 fileMenu.addSeparator();
1813 fileMenu.add(vamsasStore);
1815 fileMenu.add(saveAs);
1816 fileMenu.add(outputTextboxMenu);
1817 fileMenu.add(pageSetup);
1818 fileMenu.add(printMenuItem);
1819 fileMenu.addSeparator();
1820 fileMenu.add(jMenu2);
1821 fileMenu.add(exportFeatures);
1822 fileMenu.add(exportAnnotations);
1823 fileMenu.add(LoadtreeMenuItem);
1824 fileMenu.add(associatedData);
1825 fileMenu.addSeparator();
1826 fileMenu.add(closeMenuItem);
1827 editMenu.add(undoMenuItem);
1828 editMenu.add(redoMenuItem);
1831 editMenu.add(pasteMenu);
1832 editMenu.add(delete);
1833 editMenu.addSeparator();
1834 editMenu.add(remove2LeftMenuItem);
1835 editMenu.add(remove2RightMenuItem);
1836 editMenu.add(removeGappedColumnMenuItem);
1837 editMenu.add(removeAllGapsMenuItem);
1838 editMenu.add(removeRedundancyMenuItem);
1839 editMenu.addSeparator();
1840 // dont add these yet in the CVS build - they cannot be undone!
1841 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1842 // editMenu.add(justifyLeftMenuItem);
1843 // editMenu.add(justifyRightMenuItem);
1844 // editMenu.addSeparator();
1845 editMenu.add(padGapsMenuitem);
1846 viewMenu.add(newView);
1847 viewMenu.add(expandViews);
1848 viewMenu.add(gatherViews);
1849 viewMenu.addSeparator();
1850 viewMenu.add(jMenu3);
1851 viewMenu.add(hideMenu);
1852 viewMenu.addSeparator();
1853 viewMenu.add(followHighlightMenuItem);
1854 viewMenu.add(annotationPanelMenuItem);
1855 autoAnnMenu.add(applyAutoAnnotationSettings);
1856 autoAnnMenu.add(showConsensusHistogram);
1857 autoAnnMenu.add(showSequenceLogo);
1858 autoAnnMenu.add(normaliseSequenceLogo);
1859 autoAnnMenu.addSeparator();
1860 autoAnnMenu.add(showGroupConservation);
1861 autoAnnMenu.add(showGroupConsensus);
1862 viewMenu.add(autoAnnMenu);
1863 viewMenu.addSeparator();
1864 viewMenu.add(showSeqFeatures);
1865 // viewMenu.add(showSeqFeaturesHeight);
1867 viewMenu.add(openFeatureSettings);
1868 tooltipSettingsMenu.add(showDbRefsMenuitem);
1869 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1870 viewMenu.add(tooltipSettingsMenu);
1871 viewMenu.addSeparator();
1872 viewMenu.add(alignmentProperties);
1873 viewMenu.addSeparator();
1874 viewMenu.add(overviewMenuItem);
1875 colourMenu.add(applyToAllGroups);
1876 colourMenu.add(textColour);
1877 colourMenu.addSeparator();
1878 colourMenu.add(noColourmenuItem);
1879 colourMenu.add(clustalColour);
1880 colourMenu.add(BLOSUM62Colour);
1881 colourMenu.add(PIDColour);
1882 colourMenu.add(zappoColour);
1883 colourMenu.add(taylorColour);
1884 colourMenu.add(hydrophobicityColour);
1885 colourMenu.add(helixColour);
1886 colourMenu.add(strandColour);
1887 colourMenu.add(turnColour);
1888 colourMenu.add(buriedColour);
1889 colourMenu.add(nucleotideColour);
1890 colourMenu.add(purinePyrimidineColour);
1891 colourMenu.add(RNAInteractionColour);
1892 // colourMenu.add(covariationColour);
1893 colourMenu.add(tcoffeeColour);
1894 colourMenu.add(userDefinedColour);
1895 colourMenu.addSeparator();
1896 colourMenu.add(conservationMenuItem);
1897 colourMenu.add(modifyConservation);
1898 colourMenu.add(abovePIDThreshold);
1899 colourMenu.add(modifyPID);
1900 colourMenu.add(annotationColour);
1901 colourMenu.add(rnahelicesColour);
1902 calculateMenu.add(sort);
1903 calculateMenu.add(calculateTree);
1904 calculateMenu.addSeparator();
1905 calculateMenu.add(pairwiseAlignmentMenuItem);
1906 calculateMenu.add(PCAMenuItem);
1907 calculateMenu.addSeparator();
1908 calculateMenu.add(showTranslation);
1909 calculateMenu.add(showProducts);
1910 calculateMenu.add(autoCalculate);
1911 calculateMenu.add(sortByTree);
1912 calculateMenu.addSeparator();
1913 calculateMenu.add(extractScores);
1914 webServiceNoServices = new JMenuItem("<No Services>");
1915 webService.add(webServiceNoServices);
1916 pasteMenu.add(pasteNew);
1917 pasteMenu.add(pasteThis);
1918 sort.add(sortIDMenuItem);
1919 sort.add(sortLengthMenuItem);
1920 sort.add(sortGroupMenuItem);
1921 sort.add(sortPairwiseMenuItem);
1922 sort.add(sortByTreeMenu);
1923 calculateTree.add(averageDistanceTreeMenuItem);
1924 calculateTree.add(neighbourTreeMenuItem);
1925 calculateTree.add(avDistanceTreeBlosumMenuItem);
1926 calculateTree.add(njTreeBlosumMenuItem);
1927 jMenu2.add(htmlMenuItem);
1928 jMenu2.add(epsFile);
1929 jMenu2.add(createPNG);
1930 addSequenceMenu.add(addFromFile);
1931 addSequenceMenu.add(addFromText);
1932 addSequenceMenu.add(addFromURL);
1933 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1934 statusPanel.add(statusBar, null);
1935 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1936 jMenu3.add(showAllColumns);
1937 jMenu3.add(showAllSeqs);
1938 jMenu3.add(showAllhidden);
1939 hideMenu.add(hideSelColumns);
1940 hideMenu.add(hideSelSequences);
1941 hideMenu.add(hideAllSelection);
1942 hideMenu.add(hideAllButSelection);
1944 formatMenu.add(font);
1945 formatMenu.addSeparator();
1946 formatMenu.add(wrapMenuItem);
1947 formatMenu.add(scaleAbove);
1948 formatMenu.add(scaleLeft);
1949 formatMenu.add(scaleRight);
1950 formatMenu.add(seqLimits);
1951 formatMenu.add(idRightAlign);
1952 formatMenu.add(hiddenMarkers);
1953 formatMenu.add(viewBoxesMenuItem);
1954 formatMenu.add(viewTextMenuItem);
1955 formatMenu.add(colourTextMenuItem);
1956 formatMenu.add(renderGapsMenuItem);
1957 formatMenu.add(centreColumnLabelsMenuItem);
1958 formatMenu.add(showNonconservedMenuItem);
1959 selectMenu.add(findMenuItem);
1960 selectMenu.addSeparator();
1961 selectMenu.add(selectAllSequenceMenuItem);
1962 selectMenu.add(deselectAllSequenceMenuItem);
1963 selectMenu.add(invertSequenceMenuItem);
1964 selectMenu.add(invertColSel);
1965 selectMenu.add(deleteGroups);
1966 selectMenu.add(grpsFromSelection);
1967 // TODO - determine if the listenToViewSelections button is needed : see bug
1969 // selectMenu.addSeparator();
1970 // selectMenu.add(listenToViewSelections);
1973 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1975 // TODO Auto-generated method stub
1979 protected void listenToViewSelections_actionPerformed(ActionEvent e)
1981 // TODO Auto-generated method stub
1985 protected void showAllhidden_actionPerformed(ActionEvent e)
1987 // TODO Auto-generated method stub
1991 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1993 // TODO Auto-generated method stub
1997 protected void hideAllSelection_actionPerformed(ActionEvent e)
1999 // TODO Auto-generated method stub
2003 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2005 // TODO Auto-generated method stub
2009 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2011 // TODO Auto-generated method stub
2015 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2017 // TODO Auto-generated method stub
2021 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2023 // TODO Auto-generated method stub
2027 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2029 // TODO Auto-generated method stub
2033 protected void showGroupConservation_actionPerformed(ActionEvent e)
2035 // TODO Auto-generated method stub
2039 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2041 // TODO Auto-generated method stub
2045 protected void showSeqFeaturesHeight_actionPerformed(
2046 ActionEvent actionEvent)
2048 // TODO Auto-generated method stub
2052 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2054 // TODO Auto-generated method stub
2058 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2060 // TODO Auto-generated method stub
2064 protected void followHighlight_actionPerformed()
2066 // TODO Auto-generated method stub
2070 protected void showNpFeats_actionPerformed(ActionEvent e)
2072 // TODO Auto-generated method stub
2076 protected void showDbRefs_actionPerformed(ActionEvent e)
2078 // TODO Auto-generated method stub
2082 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2086 protected void showProducts_actionPerformed(ActionEvent e)
2090 protected void buildSortByAnnotationScoresMenu()
2094 protected void extractScores_actionPerformed(ActionEvent e)
2098 protected void outputText_actionPerformed(ActionEvent e)
2102 public void addFromFile_actionPerformed(ActionEvent e)
2107 public void addFromText_actionPerformed(ActionEvent e)
2112 public void addFromURL_actionPerformed(ActionEvent e)
2117 public void exportFeatures_actionPerformed(ActionEvent e)
2122 public void exportAnnotations_actionPerformed(ActionEvent e)
2127 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2131 protected void closeMenuItem_actionPerformed(boolean b)
2135 protected void redoMenuItem_actionPerformed(ActionEvent e)
2139 protected void undoMenuItem_actionPerformed(ActionEvent e)
2143 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2147 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2151 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2155 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2159 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2163 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2167 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2171 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2175 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2179 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2183 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2187 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2191 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2195 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2199 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2203 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2207 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2211 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2215 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2219 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2223 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2227 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2231 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2235 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2239 protected void clustalColour_actionPerformed(ActionEvent e)
2243 protected void zappoColour_actionPerformed(ActionEvent e)
2247 protected void taylorColour_actionPerformed(ActionEvent e)
2251 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2255 protected void helixColour_actionPerformed(ActionEvent e)
2259 protected void strandColour_actionPerformed(ActionEvent e)
2263 protected void turnColour_actionPerformed(ActionEvent e)
2267 protected void buriedColour_actionPerformed(ActionEvent e)
2271 protected void userDefinedColour_actionPerformed(ActionEvent e)
2275 protected void PIDColour_actionPerformed(ActionEvent e)
2279 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2283 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2287 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2293 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2296 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2300 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2304 protected void printMenuItem_actionPerformed(ActionEvent e)
2308 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2312 protected void findMenuItem_actionPerformed(ActionEvent e)
2316 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2320 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2324 protected void nucleotideColour_actionPerformed(ActionEvent e)
2328 protected void deleteGroups_actionPerformed(ActionEvent e)
2332 protected void copy_actionPerformed(ActionEvent e)
2336 protected void cut_actionPerformed(ActionEvent e)
2340 protected void delete_actionPerformed(ActionEvent e)
2344 protected void pasteNew_actionPerformed(ActionEvent e)
2348 protected void pasteThis_actionPerformed(ActionEvent e)
2352 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2356 public void createPNG(java.io.File f)
2360 protected void font_actionPerformed(ActionEvent e)
2364 protected void seqLimit_actionPerformed(ActionEvent e)
2368 public void seqDBRef_actionPerformed(ActionEvent e)
2373 public void createEPS(java.io.File f)
2377 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2383 * Template method to handle the 'load T-Coffee scores' menu event.
2385 * Subclasses override this method to provide a custom action.
2390 protected void loadScores_actionPerformed(ActionEvent event)
2396 * Template method to handle the 'Color T-Coffee scores' menu event.
2398 * Subclasses override this method to provide a custom action.
2403 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2408 protected void jpred_actionPerformed(ActionEvent e)
2412 protected void scaleAbove_actionPerformed(ActionEvent e)
2416 protected void scaleLeft_actionPerformed(ActionEvent e)
2420 protected void scaleRight_actionPerformed(ActionEvent e)
2424 protected void modifyPID_actionPerformed(ActionEvent e)
2428 protected void modifyConservation_actionPerformed(ActionEvent e)
2432 protected void saveAs_actionPerformed(ActionEvent e)
2436 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2440 public void vamsasStore_actionPerformed(ActionEvent e)
2445 public void vamsasLoad_actionPerformed(ActionEvent e)
2450 public void showTranslation_actionPerformed(ActionEvent e)
2455 public void featureSettings_actionPerformed(ActionEvent e)
2460 public void fetchSequence_actionPerformed(ActionEvent e)
2465 public void smoothFont_actionPerformed(ActionEvent e)
2470 public void annotationColour_actionPerformed(ActionEvent e)
2475 public void rnahelicesColour_actionPerformed(ActionEvent e)
2480 public void associatedData_actionPerformed(ActionEvent e)
2485 public void autoCalculate_actionPerformed(ActionEvent e)
2490 public void sortByTreeOption_actionPerformed(ActionEvent e)
2495 public void showAllSeqs_actionPerformed(ActionEvent e)
2500 public void showAllColumns_actionPerformed(ActionEvent e)
2505 public void hideSelSequences_actionPerformed(ActionEvent e)
2510 public void hideSelColumns_actionPerformed(ActionEvent e)
2515 public void hiddenMarkers_actionPerformed(ActionEvent e)
2520 public void findPdbId_actionPerformed(ActionEvent e)
2525 public void enterPdbId_actionPerformed(ActionEvent e)
2530 public void pdbFile_actionPerformed(ActionEvent e)
2535 public void invertColSel_actionPerformed(ActionEvent e)
2540 public void tabSelectionChanged(int sel)
2545 public void tabbedPane_mousePressed(MouseEvent e)
2550 public void tabbedPane_focusGained(FocusEvent e)
2555 public void save_actionPerformed(ActionEvent e)
2560 public void reload_actionPerformed(ActionEvent e)
2565 public void newView_actionPerformed(ActionEvent e)
2570 public void textColour_actionPerformed(ActionEvent e)
2575 public void idRightAlign_actionPerformed(ActionEvent e)
2580 public void expandViews_actionPerformed(ActionEvent e)
2585 public void gatherViews_actionPerformed(ActionEvent e)
2590 public void buildTreeMenu()
2595 public void pageSetup_actionPerformed(ActionEvent e)
2600 public void alignmentProperties()