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 covariationColour = new
143 // JRadioButtonMenuItem();
145 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
147 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
149 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
151 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
153 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
155 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
157 JMenuItem htmlMenuItem = new JMenuItem();
159 JMenuItem overviewMenuItem = new JMenuItem();
161 protected JMenuItem undoMenuItem = new JMenuItem();
163 protected JMenuItem redoMenuItem = new JMenuItem();
165 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
167 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
169 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
171 JMenuItem printMenuItem = new JMenuItem();
173 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
175 JMenuItem findMenuItem = new JMenuItem();
177 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
179 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
181 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
183 JMenuItem deleteGroups = new JMenuItem();
185 JMenuItem delete = new JMenuItem();
187 JMenuItem copy = new JMenuItem();
189 JMenuItem cut = new JMenuItem();
191 JMenu pasteMenu = new JMenu();
193 JMenuItem pasteNew = new JMenuItem();
195 JMenuItem pasteThis = new JMenuItem();
197 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
199 JMenuItem createPNG = new JMenuItem();
201 protected JMenuItem font = new JMenuItem();
203 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
205 JMenuItem epsFile = new JMenuItem();
207 JMenuItem LoadtreeMenuItem = new JMenuItem();
209 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
211 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
213 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
215 protected JMenuItem modifyPID = new JMenuItem();
217 protected JMenuItem modifyConservation = new JMenuItem();
219 protected JMenu sortByTreeMenu = new JMenu();
221 protected JMenu sort = new JMenu();
223 protected JMenu calculateTree = new JMenu();
225 JMenu jMenu2 = new JMenu();
227 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
229 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
231 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
233 protected ButtonGroup colours = new ButtonGroup();
235 JMenuItem vamsasStore = new JMenuItem();
237 protected JMenuItem showTranslation = new JMenuItem();
239 protected JMenuItem extractScores = new JMenuItem();
241 protected JMenu showProducts = new JMenu();
243 public JMenuItem openFeatureSettings = new JMenuItem();
245 JMenuItem fetchSequence = new JMenuItem();
247 JMenuItem annotationColour = new JMenuItem();
249 protected JMenuItem rnahelicesColour = new JMenuItem();
251 JMenuItem associatedData = new JMenuItem();
253 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
255 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
257 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
259 JMenu addSequenceMenu = new JMenu();
261 JMenuItem addFromFile = new JMenuItem();
263 JMenuItem addFromText = new JMenuItem();
265 JMenuItem addFromURL = new JMenuItem();
267 JMenuItem exportAnnotations = new JMenuItem();
269 JMenuItem exportFeatures = new JMenuItem();
271 protected JPanel statusPanel = new JPanel();
273 GridLayout gridLayout1 = new GridLayout();
275 JMenu jMenu3 = new JMenu();
277 JMenuItem showAllSeqs = new JMenuItem();
279 JMenuItem showAllColumns = new JMenuItem();
281 JMenu hideMenu = new JMenu();
283 JMenuItem hideSelSequences = new JMenuItem();
285 JMenuItem hideSelColumns = new JMenuItem();
287 JMenuItem hideAllButSelection = new JMenuItem();
289 JMenuItem hideAllSelection = new JMenuItem();
291 JMenuItem showAllhidden = new JMenuItem();
293 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
295 JMenuItem invertColSel = new JMenuItem();
297 protected JTabbedPane tabbedPane = new JTabbedPane();
299 JMenuItem save = new JMenuItem();
301 protected JMenuItem reload = new JMenuItem();
303 JMenuItem newView = new JMenuItem();
305 JMenuItem textColour = new JMenuItem();
307 JMenu formatMenu = new JMenu();
309 JMenu selectMenu = new JMenu();
311 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
313 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
315 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
317 protected JMenuItem gatherViews = new JMenuItem();
319 protected JMenuItem expandViews = new JMenuItem();
321 JMenuItem pageSetup = new JMenuItem();
323 JMenuItem alignmentProperties = new JMenuItem();
325 JMenu tooltipSettingsMenu = new JMenu();
327 private JMenuItem justifyLeftMenuItem = new JMenuItem();
329 private JMenuItem justifyRightMenuItem = new JMenuItem();
331 JMenu autoAnnMenu = new JMenu();
333 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
335 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
337 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
339 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
341 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
343 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
345 private JMenuItem grpsFromSelection = new JMenuItem();
352 setJMenuBar(alignFrameMenuBar);
354 // dynamically fill save as menu with available formats
355 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
357 JMenuItem item = new JMenuItem(
358 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
360 item.addActionListener(new java.awt.event.ActionListener()
362 public void actionPerformed(ActionEvent e)
364 outputText_actionPerformed(e);
368 outputTextboxMenu.add(item);
370 } catch (Exception e)
374 if (!new jalview.util.Platform().isAMac())
376 closeMenuItem.setMnemonic('C');
377 outputTextboxMenu.setMnemonic('T');
378 undoMenuItem.setMnemonic('Z');
379 redoMenuItem.setMnemonic('0');
380 copy.setMnemonic('C');
381 cut.setMnemonic('U');
382 pasteMenu.setMnemonic('P');
383 reload.setMnemonic('R');
386 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
388 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
389 .getUserColourSchemes().keys();
391 while (userColours.hasMoreElements())
393 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
394 userColours.nextElement().toString());
395 radioItem.setName("USER_DEFINED");
396 radioItem.addMouseListener(new MouseAdapter()
398 public void mousePressed(MouseEvent evt)
400 if (evt.isControlDown()
401 || SwingUtilities.isRightMouseButton(evt))
403 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
405 int option = JOptionPane.showInternalConfirmDialog(
406 jalview.gui.Desktop.desktop,
407 "Remove from default list?",
408 "Remove user defined colour",
409 JOptionPane.YES_NO_OPTION);
410 if (option == JOptionPane.YES_OPTION)
412 jalview.gui.UserDefinedColours
413 .removeColourFromDefaults(radioItem.getText());
414 colourMenu.remove(radioItem);
418 radioItem.addActionListener(new ActionListener()
420 public void actionPerformed(ActionEvent evt)
422 userDefinedColour_actionPerformed(evt);
429 radioItem.addActionListener(new ActionListener()
431 public void actionPerformed(ActionEvent evt)
433 userDefinedColour_actionPerformed(evt);
436 colourMenu.insert(radioItem, 15);
437 colours.add(radioItem);
440 colours.add(noColourmenuItem);
441 colours.add(clustalColour);
442 colours.add(zappoColour);
443 colours.add(taylorColour);
444 colours.add(hydrophobicityColour);
445 colours.add(helixColour);
446 colours.add(strandColour);
447 colours.add(turnColour);
448 colours.add(buriedColour);
449 colours.add(userDefinedColour);
450 colours.add(PIDColour);
451 colours.add(BLOSUM62Colour);
452 colours.add(nucleotideColour);
453 colours.add(purinePyrimidineColour);
454 // colours.add(covariationColour);
455 colours.add(tcoffeeColour);
457 setColourSelected(jalview.bin.Cache
458 .getDefault("DEFAULT_COLOUR", "None"));
462 public void setColourSelected(String defaultColour)
465 if (defaultColour != null)
467 int index = ColourSchemeProperty
468 .getColourIndexFromName(defaultColour);
472 case ColourSchemeProperty.CLUSTAL:
473 clustalColour.setSelected(true);
477 case ColourSchemeProperty.BLOSUM:
478 BLOSUM62Colour.setSelected(true);
482 case ColourSchemeProperty.PID:
483 PIDColour.setSelected(true);
487 case ColourSchemeProperty.ZAPPO:
488 zappoColour.setSelected(true);
492 case ColourSchemeProperty.TAYLOR:
493 taylorColour.setSelected(true);
496 case ColourSchemeProperty.HYDROPHOBIC:
497 hydrophobicityColour.setSelected(true);
501 case ColourSchemeProperty.HELIX:
502 helixColour.setSelected(true);
506 case ColourSchemeProperty.STRAND:
507 strandColour.setSelected(true);
511 case ColourSchemeProperty.TURN:
512 turnColour.setSelected(true);
516 case ColourSchemeProperty.BURIED:
517 buriedColour.setSelected(true);
521 case ColourSchemeProperty.NUCLEOTIDE:
522 nucleotideColour.setSelected(true);
526 case ColourSchemeProperty.TCOFFEE:
527 tcoffeeColour.setSelected(true);
530 case ColourSchemeProperty.PURINEPYRIMIDINE:
531 purinePyrimidineColour.setSelected(true);
535 * case ColourSchemeProperty.COVARIATION:
536 * covariationColour.setSelected(true);
540 case ColourSchemeProperty.USER_DEFINED:
541 userDefinedColour.setSelected(true);
544 case ColourSchemeProperty.NONE:
546 noColourmenuItem.setSelected(true);
554 private void jbInit() throws Exception
556 fileMenu.setText("File");
557 saveAs.setText("Save As...");
558 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
559 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
560 .getMenuShortcutKeyMask()
561 | java.awt.event.KeyEvent.SHIFT_MASK, false));
562 saveAs.addActionListener(new ActionListener()
564 public void actionPerformed(ActionEvent e)
566 saveAs_actionPerformed(e);
569 closeMenuItem.setText("Close");
570 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
571 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
572 .getMenuShortcutKeyMask(), false));
573 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
575 public void actionPerformed(ActionEvent e)
577 closeMenuItem_actionPerformed(false);
580 editMenu.setText("Edit");
581 viewMenu.setText("View");
582 colourMenu.setText("Colour");
583 calculateMenu.setText("Calculate");
584 webService.setText("Web Service");
585 selectAllSequenceMenuItem.setText("Select All");
586 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
587 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
588 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
589 selectAllSequenceMenuItem
590 .addActionListener(new java.awt.event.ActionListener()
592 public void actionPerformed(ActionEvent e)
594 selectAllSequenceMenuItem_actionPerformed(e);
597 deselectAllSequenceMenuItem.setText("Deselect All");
598 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
599 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
600 deselectAllSequenceMenuItem
601 .addActionListener(new java.awt.event.ActionListener()
603 public void actionPerformed(ActionEvent e)
605 deselectAllSequenceMenuItem_actionPerformed(e);
608 invertSequenceMenuItem.setText("Invert Sequence Selection");
609 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
610 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
611 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
612 invertSequenceMenuItem
613 .addActionListener(new java.awt.event.ActionListener()
615 public void actionPerformed(ActionEvent e)
617 invertSequenceMenuItem_actionPerformed(e);
620 grpsFromSelection.setText("Make Groups for selection");
621 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
623 public void actionPerformed(ActionEvent e)
625 makeGrpsFromSelection_actionPerformed(e);
629 remove2LeftMenuItem.setText("Remove Left");
630 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
631 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
632 .getMenuShortcutKeyMask(), false));
634 .addActionListener(new java.awt.event.ActionListener()
636 public void actionPerformed(ActionEvent e)
638 remove2LeftMenuItem_actionPerformed(e);
641 remove2RightMenuItem.setText("Remove Right");
642 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
643 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
644 .getMenuShortcutKeyMask(), false));
646 .addActionListener(new java.awt.event.ActionListener()
648 public void actionPerformed(ActionEvent e)
650 remove2RightMenuItem_actionPerformed(e);
653 removeGappedColumnMenuItem.setText("Remove Empty Columns");
654 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
655 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
656 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
657 removeGappedColumnMenuItem
658 .addActionListener(new java.awt.event.ActionListener()
660 public void actionPerformed(ActionEvent e)
662 removeGappedColumnMenuItem_actionPerformed(e);
665 removeAllGapsMenuItem.setText("Remove All Gaps");
666 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
667 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
668 .getDefaultToolkit().getMenuShortcutKeyMask()
669 | java.awt.event.KeyEvent.SHIFT_MASK, false));
670 removeAllGapsMenuItem
671 .addActionListener(new java.awt.event.ActionListener()
673 public void actionPerformed(ActionEvent e)
675 removeAllGapsMenuItem_actionPerformed(e);
678 justifyLeftMenuItem.setText("Left Justify Alignment");
680 .addActionListener(new java.awt.event.ActionListener()
682 public void actionPerformed(ActionEvent e)
684 justifyLeftMenuItem_actionPerformed(e);
687 justifyRightMenuItem.setText("Right Justify Alignment");
689 .addActionListener(new java.awt.event.ActionListener()
691 public void actionPerformed(ActionEvent e)
693 justifyRightMenuItem_actionPerformed(e);
696 viewBoxesMenuItem.setText("Boxes");
697 viewBoxesMenuItem.setState(true);
698 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
700 public void actionPerformed(ActionEvent e)
702 viewBoxesMenuItem_actionPerformed(e);
705 viewTextMenuItem.setText("Text");
706 viewTextMenuItem.setState(true);
707 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
709 public void actionPerformed(ActionEvent e)
711 viewTextMenuItem_actionPerformed(e);
714 showNonconservedMenuItem.setText("Show nonconserved");
715 showNonconservedMenuItem.setState(false);
716 showNonconservedMenuItem
717 .addActionListener(new java.awt.event.ActionListener()
719 public void actionPerformed(ActionEvent e)
721 showUnconservedMenuItem_actionPerformed(e);
724 sortPairwiseMenuItem.setText("by Pairwise Identity");
726 .addActionListener(new java.awt.event.ActionListener()
728 public void actionPerformed(ActionEvent e)
730 sortPairwiseMenuItem_actionPerformed(e);
733 sortIDMenuItem.setText("by ID");
734 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
736 public void actionPerformed(ActionEvent e)
738 sortIDMenuItem_actionPerformed(e);
741 sortLengthMenuItem.setText("By Length");
743 .addActionListener(new java.awt.event.ActionListener()
745 public void actionPerformed(ActionEvent e)
747 sortLengthMenuItem_actionPerformed(e);
750 sortGroupMenuItem.setText("by Group");
751 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
753 public void actionPerformed(ActionEvent e)
755 sortGroupMenuItem_actionPerformed(e);
758 removeRedundancyMenuItem.setText("Remove Redundancy...");
759 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
760 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
761 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
762 removeRedundancyMenuItem
763 .addActionListener(new java.awt.event.ActionListener()
765 public void actionPerformed(ActionEvent e)
767 removeRedundancyMenuItem_actionPerformed(e);
770 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
771 pairwiseAlignmentMenuItem
772 .addActionListener(new java.awt.event.ActionListener()
774 public void actionPerformed(ActionEvent e)
776 pairwiseAlignmentMenuItem_actionPerformed(e);
779 PCAMenuItem.setText("Principal Component Analysis");
780 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
782 public void actionPerformed(ActionEvent e)
784 PCAMenuItem_actionPerformed(e);
787 averageDistanceTreeMenuItem
788 .setText("Average Distance Using % Identity");
789 averageDistanceTreeMenuItem
790 .addActionListener(new java.awt.event.ActionListener()
792 public void actionPerformed(ActionEvent e)
794 averageDistanceTreeMenuItem_actionPerformed(e);
797 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
798 neighbourTreeMenuItem
799 .addActionListener(new java.awt.event.ActionListener()
801 public void actionPerformed(ActionEvent e)
803 neighbourTreeMenuItem_actionPerformed(e);
806 this.getContentPane().setLayout(borderLayout1);
807 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
808 statusBar.setBackground(Color.white);
809 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
810 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
811 statusBar.setText("Status bar");
812 outputTextboxMenu.setText("Output to Textbox");
813 clustalColour.setText("Clustalx");
815 clustalColour.addActionListener(new java.awt.event.ActionListener()
817 public void actionPerformed(ActionEvent e)
819 clustalColour_actionPerformed(e);
822 zappoColour.setText("Zappo");
823 zappoColour.addActionListener(new java.awt.event.ActionListener()
825 public void actionPerformed(ActionEvent e)
827 zappoColour_actionPerformed(e);
830 taylorColour.setText("Taylor");
831 taylorColour.addActionListener(new java.awt.event.ActionListener()
833 public void actionPerformed(ActionEvent e)
835 taylorColour_actionPerformed(e);
838 hydrophobicityColour.setText("Hydrophobicity");
840 .addActionListener(new java.awt.event.ActionListener()
842 public void actionPerformed(ActionEvent e)
844 hydrophobicityColour_actionPerformed(e);
847 helixColour.setText("Helix Propensity");
848 helixColour.addActionListener(new java.awt.event.ActionListener()
850 public void actionPerformed(ActionEvent e)
852 helixColour_actionPerformed(e);
855 strandColour.setText("Strand Propensity");
856 strandColour.addActionListener(new java.awt.event.ActionListener()
858 public void actionPerformed(ActionEvent e)
860 strandColour_actionPerformed(e);
863 turnColour.setText("Turn Propensity");
864 turnColour.addActionListener(new java.awt.event.ActionListener()
866 public void actionPerformed(ActionEvent e)
868 turnColour_actionPerformed(e);
871 buriedColour.setText("Buried Index");
872 buriedColour.addActionListener(new java.awt.event.ActionListener()
874 public void actionPerformed(ActionEvent e)
876 buriedColour_actionPerformed(e);
879 userDefinedColour.setText("User Defined...");
880 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
882 public void actionPerformed(ActionEvent e)
884 userDefinedColour_actionPerformed(e);
887 PIDColour.setText("Percentage Identity");
888 PIDColour.addActionListener(new java.awt.event.ActionListener()
890 public void actionPerformed(ActionEvent e)
892 PIDColour_actionPerformed(e);
895 BLOSUM62Colour.setText("BLOSUM62 Score");
896 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
898 public void actionPerformed(ActionEvent e)
900 BLOSUM62Colour_actionPerformed(e);
903 nucleotideColour.setText("Nucleotide");
904 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
906 public void actionPerformed(ActionEvent e)
908 nucleotideColour_actionPerformed(e);
912 purinePyrimidineColour.setText("Purine/Pyrimidine");
913 purinePyrimidineColour
914 .addActionListener(new java.awt.event.ActionListener()
916 public void actionPerformed(ActionEvent e)
918 purinePyrimidineColour_actionPerformed(e);
922 * covariationColour.setText("Covariation");
923 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
924 * public void actionPerformed(ActionEvent e) {
925 * covariationColour_actionPerformed(e); } });
928 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
929 avDistanceTreeBlosumMenuItem
930 .addActionListener(new java.awt.event.ActionListener()
932 public void actionPerformed(ActionEvent e)
934 avTreeBlosumMenuItem_actionPerformed(e);
937 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
939 .addActionListener(new java.awt.event.ActionListener()
941 public void actionPerformed(ActionEvent e)
943 njTreeBlosumMenuItem_actionPerformed(e);
946 annotationPanelMenuItem.setActionCommand("");
947 annotationPanelMenuItem.setText("Show Annotations");
948 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
949 "SHOW_ANNOTATIONS", true));
950 annotationPanelMenuItem
951 .addActionListener(new java.awt.event.ActionListener()
953 public void actionPerformed(ActionEvent e)
955 annotationPanelMenuItem_actionPerformed(e);
958 colourTextMenuItem.setText("Colour Text");
960 .addActionListener(new java.awt.event.ActionListener()
962 public void actionPerformed(ActionEvent e)
964 colourTextMenuItem_actionPerformed(e);
967 htmlMenuItem.setText("HTML");
968 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
970 public void actionPerformed(ActionEvent e)
972 htmlMenuItem_actionPerformed(e);
975 overviewMenuItem.setText("Overview Window");
976 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
978 public void actionPerformed(ActionEvent e)
980 overviewMenuItem_actionPerformed(e);
983 undoMenuItem.setEnabled(false);
984 undoMenuItem.setText("Undo");
985 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
986 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
987 .getMenuShortcutKeyMask(), false));
988 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
990 public void actionPerformed(ActionEvent e)
992 undoMenuItem_actionPerformed(e);
995 redoMenuItem.setEnabled(false);
996 redoMenuItem.setText("Redo");
997 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
998 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
999 .getMenuShortcutKeyMask(), false));
1000 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1002 public void actionPerformed(ActionEvent e)
1004 redoMenuItem_actionPerformed(e);
1007 conservationMenuItem.setText("By Conservation");
1008 conservationMenuItem
1009 .addActionListener(new java.awt.event.ActionListener()
1011 public void actionPerformed(ActionEvent e)
1013 conservationMenuItem_actionPerformed(e);
1016 noColourmenuItem.setText("None");
1017 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1019 public void actionPerformed(ActionEvent e)
1021 noColourmenuItem_actionPerformed(e);
1024 wrapMenuItem.setText("Wrap");
1025 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1027 public void actionPerformed(ActionEvent e)
1029 wrapMenuItem_actionPerformed(e);
1032 printMenuItem.setText("Print ...");
1033 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1034 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1035 .getMenuShortcutKeyMask(), false));
1036 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1038 public void actionPerformed(ActionEvent e)
1040 printMenuItem_actionPerformed(e);
1043 renderGapsMenuItem.setText("Show Gaps");
1044 renderGapsMenuItem.setState(true);
1046 .addActionListener(new java.awt.event.ActionListener()
1048 public void actionPerformed(ActionEvent e)
1050 renderGapsMenuItem_actionPerformed(e);
1053 findMenuItem.setText("Find...");
1054 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1055 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1056 .getMenuShortcutKeyMask(), false));
1057 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1059 public void actionPerformed(ActionEvent e)
1061 findMenuItem_actionPerformed(e);
1064 abovePIDThreshold.setText("Above Identity Threshold");
1065 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1067 public void actionPerformed(ActionEvent e)
1069 abovePIDThreshold_actionPerformed(e);
1072 showSeqFeatures.setText("Show Sequence Features");
1073 showSeqFeatures.addActionListener(new ActionListener()
1075 public void actionPerformed(ActionEvent actionEvent)
1077 showSeqFeatures_actionPerformed(actionEvent);
1081 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1082 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1083 * void actionPerformed(ActionEvent actionEvent) {
1084 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1086 showDbRefsMenuitem.setText("Show Database Refs");
1087 showDbRefsMenuitem.addActionListener(new ActionListener()
1090 public void actionPerformed(ActionEvent e)
1092 showDbRefs_actionPerformed(e);
1096 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1097 showNpFeatsMenuitem.addActionListener(new ActionListener()
1100 public void actionPerformed(ActionEvent e)
1102 showNpFeats_actionPerformed(e);
1106 showGroupConservation.setText("Group Conservation");
1107 showGroupConservation.addActionListener(new ActionListener()
1110 public void actionPerformed(ActionEvent e)
1112 showGroupConservation_actionPerformed(e);
1117 showGroupConsensus.setText("Group Consensus");
1118 showGroupConsensus.addActionListener(new ActionListener()
1121 public void actionPerformed(ActionEvent e)
1123 showGroupConsensus_actionPerformed(e);
1127 showConsensusHistogram.setText("Show Consensus Histogram");
1128 showConsensusHistogram.addActionListener(new ActionListener()
1131 public void actionPerformed(ActionEvent e)
1133 showConsensusHistogram_actionPerformed(e);
1137 showSequenceLogo.setText("Show Consensus Logo");
1138 showSequenceLogo.addActionListener(new ActionListener()
1141 public void actionPerformed(ActionEvent e)
1143 showSequenceLogo_actionPerformed(e);
1147 normaliseSequenceLogo.setText("Normalise Consensus Logo");
1148 normaliseSequenceLogo.addActionListener(new ActionListener()
1151 public void actionPerformed(ActionEvent e)
1153 normaliseSequenceLogo_actionPerformed(e);
1157 applyAutoAnnotationSettings.setText("Apply to all groups");
1158 applyAutoAnnotationSettings.setState(false);
1159 applyAutoAnnotationSettings.setVisible(true);
1160 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1163 public void actionPerformed(ActionEvent e)
1165 applyAutoAnnotationSettings_actionPerformed(e);
1170 nucleotideColour.setText("Nucleotide");
1171 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1173 public void actionPerformed(ActionEvent e)
1175 nucleotideColour_actionPerformed(e);
1179 tcoffeeColour.setText("T-Coffee scores");
1180 tcoffeeColour.setEnabled(false);
1181 tcoffeeColour.addActionListener(new ActionListener()
1185 public void actionPerformed(ActionEvent e)
1187 tcoffeeColorScheme_actionPerformed(e);
1191 deleteGroups.setText("Undefine groups");
1192 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1193 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1194 .getMenuShortcutKeyMask(), false));
1195 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1197 public void actionPerformed(ActionEvent e)
1199 deleteGroups_actionPerformed(e);
1202 copy.setText("Copy");
1203 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1204 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1205 .getMenuShortcutKeyMask(), false));
1207 copy.addActionListener(new java.awt.event.ActionListener()
1209 public void actionPerformed(ActionEvent e)
1211 copy_actionPerformed(e);
1215 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1216 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1217 .getMenuShortcutKeyMask(), false));
1218 cut.addActionListener(new java.awt.event.ActionListener()
1220 public void actionPerformed(ActionEvent e)
1222 cut_actionPerformed(e);
1225 delete.setText("Delete");
1226 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1227 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1228 delete.addActionListener(new java.awt.event.ActionListener()
1230 public void actionPerformed(ActionEvent e)
1232 delete_actionPerformed(e);
1235 pasteMenu.setText("Paste");
1236 pasteNew.setText("To New Alignment");
1237 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1238 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1239 .getMenuShortcutKeyMask()
1240 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1241 pasteNew.addActionListener(new java.awt.event.ActionListener()
1243 public void actionPerformed(ActionEvent e)
1245 pasteNew_actionPerformed(e);
1248 pasteThis.setText("Add To This Alignment");
1249 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1250 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1251 .getMenuShortcutKeyMask(), false));
1252 pasteThis.addActionListener(new java.awt.event.ActionListener()
1254 public void actionPerformed(ActionEvent e)
1256 pasteThis_actionPerformed(e);
1259 applyToAllGroups.setText("Apply Colour To All Groups");
1260 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1262 public void actionPerformed(ActionEvent e)
1264 applyToAllGroups_actionPerformed(e);
1267 createPNG.addActionListener(new java.awt.event.ActionListener()
1269 public void actionPerformed(ActionEvent e)
1274 createPNG.setActionCommand("Save As PNG Image");
1275 createPNG.setText("PNG");
1276 font.setText("Font...");
1277 font.addActionListener(new java.awt.event.ActionListener()
1279 public void actionPerformed(ActionEvent e)
1281 font_actionPerformed(e);
1285 seqLimits.setText("Show Sequence Limits");
1286 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1287 seqLimits.addActionListener(new java.awt.event.ActionListener()
1289 public void actionPerformed(ActionEvent e)
1291 seqLimit_actionPerformed(e);
1294 epsFile.setText("EPS");
1295 epsFile.addActionListener(new java.awt.event.ActionListener()
1297 public void actionPerformed(ActionEvent e)
1302 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1303 LoadtreeMenuItem.setText("Load Associated Tree");
1304 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1306 public void actionPerformed(ActionEvent e)
1308 LoadtreeMenuItem_actionPerformed(e);
1312 scaleAbove.setVisible(false);
1313 scaleAbove.setText("Scale Above");
1314 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1316 public void actionPerformed(ActionEvent e)
1318 scaleAbove_actionPerformed(e);
1321 scaleLeft.setVisible(false);
1322 scaleLeft.setSelected(true);
1323 scaleLeft.setText("Scale Left");
1324 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1326 public void actionPerformed(ActionEvent e)
1328 scaleLeft_actionPerformed(e);
1331 scaleRight.setVisible(false);
1332 scaleRight.setSelected(true);
1333 scaleRight.setText("Scale Right");
1334 scaleRight.addActionListener(new java.awt.event.ActionListener()
1336 public void actionPerformed(ActionEvent e)
1338 scaleRight_actionPerformed(e);
1341 centreColumnLabelsMenuItem.setVisible(true);
1342 centreColumnLabelsMenuItem.setState(false);
1343 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1344 centreColumnLabelsMenuItem
1345 .addActionListener(new java.awt.event.ActionListener()
1347 public void actionPerformed(ActionEvent e)
1349 centreColumnLabels_actionPerformed(e);
1352 followHighlightMenuItem.setVisible(true);
1353 followHighlightMenuItem.setState(true);
1354 followHighlightMenuItem.setText("Automatic Scrolling");
1355 followHighlightMenuItem.addActionListener(new ActionListener()
1358 public void actionPerformed(ActionEvent e)
1360 followHighlight_actionPerformed();
1365 modifyPID.setText("Modify Identity Threshold...");
1366 modifyPID.addActionListener(new java.awt.event.ActionListener()
1368 public void actionPerformed(ActionEvent e)
1370 modifyPID_actionPerformed(e);
1373 modifyConservation.setText("Modify Conservation Threshold...");
1375 .addActionListener(new java.awt.event.ActionListener()
1377 public void actionPerformed(ActionEvent e)
1379 modifyConservation_actionPerformed(e);
1382 sortByTreeMenu.setText("By Tree Order");
1383 sort.setText("Sort");
1384 sort.addMenuListener(new MenuListener()
1386 public void menuSelected(MenuEvent e)
1391 public void menuDeselected(MenuEvent e)
1395 public void menuCanceled(MenuEvent e)
1399 sortByAnnotScore.setText("by Score");
1400 sort.add(sortByAnnotScore);
1401 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1404 public void menuCanceled(MenuEvent e)
1408 public void menuDeselected(MenuEvent e)
1412 public void menuSelected(MenuEvent e)
1414 buildSortByAnnotationScoresMenu();
1417 sortByAnnotScore.setVisible(false);
1419 calculateTree.setText("Calculate Tree");
1421 jMenu2.setText("Export Image");
1422 padGapsMenuitem.setText("Pad Gaps");
1423 padGapsMenuitem.setState(jalview.bin.Cache
1424 .getDefault("PAD_GAPS", false));
1425 padGapsMenuitem.addActionListener(new ActionListener()
1427 public void actionPerformed(ActionEvent e)
1429 padGapsMenuitem_actionPerformed(e);
1432 vamsasStore.setVisible(false);
1433 vamsasStore.setText("VAMSAS store");
1434 vamsasStore.addActionListener(new ActionListener()
1436 public void actionPerformed(ActionEvent e)
1438 vamsasStore_actionPerformed(e);
1441 showTranslation.setText("Translate cDNA");
1442 showTranslation.addActionListener(new ActionListener()
1444 public void actionPerformed(ActionEvent e)
1446 showTranslation_actionPerformed(e);
1449 extractScores.setText("Extract Scores...");
1450 extractScores.addActionListener(new ActionListener()
1452 public void actionPerformed(ActionEvent e)
1454 extractScores_actionPerformed(e);
1457 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1459 showProducts.setText("Get Cross References");
1461 * showProducts.addActionListener(new ActionListener() {
1463 * public void actionPerformed(ActionEvent e) {
1464 * showProducts_actionPerformed(e); } });
1466 openFeatureSettings.setText("Feature Settings...");
1467 openFeatureSettings.addActionListener(new ActionListener()
1469 public void actionPerformed(ActionEvent e)
1471 featureSettings_actionPerformed(e);
1474 fetchSequence.setText("Fetch Sequence(s)...");
1475 fetchSequence.addActionListener(new ActionListener()
1477 public void actionPerformed(ActionEvent e)
1479 fetchSequence_actionPerformed(e);
1483 annotationColour.setText("By Annotation...");
1484 annotationColour.addActionListener(new ActionListener()
1486 public void actionPerformed(ActionEvent e)
1488 annotationColour_actionPerformed(e);
1492 rnahelicesColour.setText("By RNA helices");
1493 rnahelicesColour.addActionListener(new ActionListener()
1495 public void actionPerformed(ActionEvent e)
1497 rnahelicesColour_actionPerformed(e);
1501 associatedData.setText("Load Features / Annotations");
1502 associatedData.addActionListener(new ActionListener()
1504 public void actionPerformed(ActionEvent e)
1506 associatedData_actionPerformed(e);
1509 autoCalculate.setText("Autocalculate Consensus");
1510 autoCalculate.setState(jalview.bin.Cache.getDefault(
1511 "AUTO_CALC_CONSENSUS", true));
1512 autoCalculate.addActionListener(new ActionListener()
1514 public void actionPerformed(ActionEvent e)
1516 autoCalculate_actionPerformed(e);
1519 sortByTree.setText("Sort Alignment With New Tree");
1521 .setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1523 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1524 sortByTree.addActionListener(new ActionListener()
1526 public void actionPerformed(ActionEvent e)
1528 sortByTreeOption_actionPerformed(e);
1532 listenToViewSelections.setText("Listen for selections");
1533 listenToViewSelections
1534 .setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1535 listenToViewSelections.setState(false);
1536 listenToViewSelections.addActionListener(new ActionListener()
1538 public void actionPerformed(ActionEvent e)
1540 listenToViewSelections_actionPerformed(e);
1544 addSequenceMenu.setText("Add Sequences");
1545 addFromFile.setText("From File");
1546 addFromFile.addActionListener(new ActionListener()
1548 public void actionPerformed(ActionEvent e)
1550 addFromFile_actionPerformed(e);
1553 addFromText.setText("From Textbox");
1554 addFromText.addActionListener(new ActionListener()
1556 public void actionPerformed(ActionEvent e)
1558 addFromText_actionPerformed(e);
1561 addFromURL.setText("From URL");
1562 addFromURL.addActionListener(new ActionListener()
1564 public void actionPerformed(ActionEvent e)
1566 addFromURL_actionPerformed(e);
1569 exportFeatures.setText("Export Features...");
1570 exportFeatures.addActionListener(new ActionListener()
1572 public void actionPerformed(ActionEvent e)
1574 exportFeatures_actionPerformed(e);
1577 exportAnnotations.setText("Export Annotations...");
1578 exportAnnotations.addActionListener(new ActionListener()
1580 public void actionPerformed(ActionEvent e)
1582 exportAnnotations_actionPerformed(e);
1585 statusPanel.setLayout(gridLayout1);
1586 jMenu3.setText("Show");
1587 showAllSeqs.setText("All Sequences");
1588 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1589 showAllSeqs.addActionListener(new ActionListener()
1591 public void actionPerformed(ActionEvent e)
1593 showAllSeqs_actionPerformed(e);
1596 showAllColumns.setText("All Columns");
1597 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1598 showAllColumns.addActionListener(new ActionListener()
1600 public void actionPerformed(ActionEvent e)
1602 showAllColumns_actionPerformed(e);
1605 hideMenu.setText("Hide");
1606 hideSelSequences.setText("Selected Sequences");
1607 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1608 hideSelSequences.addActionListener(new ActionListener()
1610 public void actionPerformed(ActionEvent e)
1612 hideSelSequences_actionPerformed(e);
1615 hideSelColumns.setText("Selected Columns");
1616 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1617 hideSelColumns.addActionListener(new ActionListener()
1619 public void actionPerformed(ActionEvent e)
1621 hideSelColumns_actionPerformed(e);
1624 hideAllSelection.setText("Selected Region");
1625 hideAllSelection.addActionListener(new ActionListener()
1627 public void actionPerformed(ActionEvent e)
1629 hideAllSelection_actionPerformed(e);
1632 // TODO: should be hidden if no selection exists.
1633 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1634 hideAllButSelection.addActionListener(new ActionListener()
1636 public void actionPerformed(ActionEvent e)
1638 hideAllButSelection_actionPerformed(e);
1641 showAllhidden.setText("All Sequences and Columns");
1643 .setToolTipText("H toggles visibility of hidden or selected regions.");
1644 showAllhidden.addActionListener(new ActionListener()
1646 public void actionPerformed(ActionEvent e)
1648 showAllhidden_actionPerformed(e);
1652 hiddenMarkers.setText("Show Hidden Markers");
1653 hiddenMarkers.addActionListener(new ActionListener()
1655 public void actionPerformed(ActionEvent e)
1657 hiddenMarkers_actionPerformed(e);
1660 invertColSel.setText("Invert Column Selection");
1661 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1662 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1663 .getMenuShortcutKeyMask()
1664 | java.awt.event.KeyEvent.ALT_MASK, false));
1665 invertColSel.addActionListener(new ActionListener()
1667 public void actionPerformed(ActionEvent e)
1669 invertColSel_actionPerformed(e);
1672 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1674 public void stateChanged(ChangeEvent evt)
1676 JTabbedPane pane = (JTabbedPane) evt.getSource();
1677 int sel = pane.getSelectedIndex();
1678 tabSelectionChanged(sel);
1681 tabbedPane.addMouseListener(new MouseAdapter()
1683 public void mousePressed(MouseEvent e)
1685 tabbedPane_mousePressed(e);
1688 tabbedPane.addFocusListener(new FocusAdapter()
1690 public void focusGained(FocusEvent e)
1692 tabbedPane_focusGained(e);
1695 save.setText("Save");
1696 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1697 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1698 .getMenuShortcutKeyMask(), false));
1699 save.addActionListener(new ActionListener()
1701 public void actionPerformed(ActionEvent e)
1703 save_actionPerformed(e);
1706 reload.setEnabled(false);
1707 reload.setText("Reload");
1708 reload.addActionListener(new ActionListener()
1710 public void actionPerformed(ActionEvent e)
1712 reload_actionPerformed(e);
1715 newView.setText("New View");
1716 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1717 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1718 .getMenuShortcutKeyMask(), false));
1719 newView.addActionListener(new ActionListener()
1721 public void actionPerformed(ActionEvent e)
1723 newView_actionPerformed(e);
1726 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1727 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1728 textColour.setText("Colour Text ...");
1729 textColour.addActionListener(new ActionListener()
1731 public void actionPerformed(ActionEvent e)
1733 textColour_actionPerformed(e);
1736 formatMenu.setText("Format");
1737 selectMenu.setText("Select");
1738 idRightAlign.setText("Right Align Sequence Id");
1739 idRightAlign.addActionListener(new ActionListener()
1741 public void actionPerformed(ActionEvent e)
1743 idRightAlign_actionPerformed(e);
1746 gatherViews.setEnabled(false);
1747 gatherViews.setText("Gather Views");
1748 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1749 java.awt.event.KeyEvent.VK_G, 0, false));
1750 gatherViews.addActionListener(new ActionListener()
1752 public void actionPerformed(ActionEvent e)
1754 gatherViews_actionPerformed(e);
1757 expandViews.setEnabled(false);
1758 expandViews.setText("Expand Views");
1759 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1760 java.awt.event.KeyEvent.VK_X, 0, false));
1761 expandViews.addActionListener(new ActionListener()
1763 public void actionPerformed(ActionEvent e)
1765 expandViews_actionPerformed(e);
1768 pageSetup.setText("Page Setup ...");
1769 pageSetup.addActionListener(new ActionListener()
1771 public void actionPerformed(ActionEvent e)
1773 pageSetup_actionPerformed(e);
1776 alignmentProperties.setText("Alignment Properties...");
1777 alignmentProperties.addActionListener(new ActionListener()
1779 public void actionPerformed(ActionEvent actionEvent)
1781 alignmentProperties();
1784 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1785 autoAnnMenu.setText("Autocalculated Annotation");
1786 alignFrameMenuBar.add(fileMenu);
1787 alignFrameMenuBar.add(editMenu);
1788 alignFrameMenuBar.add(selectMenu);
1789 alignFrameMenuBar.add(viewMenu);
1790 alignFrameMenuBar.add(formatMenu);
1791 alignFrameMenuBar.add(colourMenu);
1792 alignFrameMenuBar.add(calculateMenu);
1793 alignFrameMenuBar.add(webService);
1794 fileMenu.add(fetchSequence);
1795 fileMenu.add(addSequenceMenu);
1796 fileMenu.add(reload);
1797 fileMenu.addSeparator();
1798 fileMenu.add(vamsasStore);
1800 fileMenu.add(saveAs);
1801 fileMenu.add(outputTextboxMenu);
1802 fileMenu.add(pageSetup);
1803 fileMenu.add(printMenuItem);
1804 fileMenu.addSeparator();
1805 fileMenu.add(jMenu2);
1806 fileMenu.add(exportFeatures);
1807 fileMenu.add(exportAnnotations);
1808 fileMenu.add(LoadtreeMenuItem);
1809 fileMenu.add(associatedData);
1810 fileMenu.addSeparator();
1811 fileMenu.add(closeMenuItem);
1812 editMenu.add(undoMenuItem);
1813 editMenu.add(redoMenuItem);
1816 editMenu.add(pasteMenu);
1817 editMenu.add(delete);
1818 editMenu.addSeparator();
1819 editMenu.add(remove2LeftMenuItem);
1820 editMenu.add(remove2RightMenuItem);
1821 editMenu.add(removeGappedColumnMenuItem);
1822 editMenu.add(removeAllGapsMenuItem);
1823 editMenu.add(removeRedundancyMenuItem);
1824 editMenu.addSeparator();
1825 // dont add these yet in the CVS build - they cannot be undone!
1826 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1827 // editMenu.add(justifyLeftMenuItem);
1828 // editMenu.add(justifyRightMenuItem);
1829 // editMenu.addSeparator();
1830 editMenu.add(padGapsMenuitem);
1831 viewMenu.add(newView);
1832 viewMenu.add(expandViews);
1833 viewMenu.add(gatherViews);
1834 viewMenu.addSeparator();
1835 viewMenu.add(jMenu3);
1836 viewMenu.add(hideMenu);
1837 viewMenu.addSeparator();
1838 viewMenu.add(followHighlightMenuItem);
1839 viewMenu.add(annotationPanelMenuItem);
1840 autoAnnMenu.add(applyAutoAnnotationSettings);
1841 autoAnnMenu.add(showConsensusHistogram);
1842 autoAnnMenu.add(showSequenceLogo);
1843 autoAnnMenu.add(normaliseSequenceLogo);
1844 autoAnnMenu.addSeparator();
1845 autoAnnMenu.add(showGroupConservation);
1846 autoAnnMenu.add(showGroupConsensus);
1847 viewMenu.add(autoAnnMenu);
1848 viewMenu.addSeparator();
1849 viewMenu.add(showSeqFeatures);
1850 // viewMenu.add(showSeqFeaturesHeight);
1852 viewMenu.add(openFeatureSettings);
1853 tooltipSettingsMenu.add(showDbRefsMenuitem);
1854 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1855 viewMenu.add(tooltipSettingsMenu);
1856 viewMenu.addSeparator();
1857 viewMenu.add(alignmentProperties);
1858 viewMenu.addSeparator();
1859 viewMenu.add(overviewMenuItem);
1860 colourMenu.add(applyToAllGroups);
1861 colourMenu.add(textColour);
1862 colourMenu.addSeparator();
1863 colourMenu.add(noColourmenuItem);
1864 colourMenu.add(clustalColour);
1865 colourMenu.add(BLOSUM62Colour);
1866 colourMenu.add(PIDColour);
1867 colourMenu.add(zappoColour);
1868 colourMenu.add(taylorColour);
1869 colourMenu.add(hydrophobicityColour);
1870 colourMenu.add(helixColour);
1871 colourMenu.add(strandColour);
1872 colourMenu.add(turnColour);
1873 colourMenu.add(buriedColour);
1874 colourMenu.add(nucleotideColour);
1875 colourMenu.add(purinePyrimidineColour);
1876 // colourMenu.add(covariationColour);
1877 colourMenu.add(tcoffeeColour);
1878 colourMenu.add(userDefinedColour);
1879 colourMenu.addSeparator();
1880 colourMenu.add(conservationMenuItem);
1881 colourMenu.add(modifyConservation);
1882 colourMenu.add(abovePIDThreshold);
1883 colourMenu.add(modifyPID);
1884 colourMenu.add(annotationColour);
1885 colourMenu.add(rnahelicesColour);
1886 calculateMenu.add(sort);
1887 calculateMenu.add(calculateTree);
1888 calculateMenu.addSeparator();
1889 calculateMenu.add(pairwiseAlignmentMenuItem);
1890 calculateMenu.add(PCAMenuItem);
1891 calculateMenu.addSeparator();
1892 calculateMenu.add(showTranslation);
1893 calculateMenu.add(showProducts);
1894 calculateMenu.add(autoCalculate);
1895 calculateMenu.add(sortByTree);
1896 calculateMenu.addSeparator();
1897 calculateMenu.add(extractScores);
1898 webServiceNoServices = new JMenuItem("<No Services>");
1899 webService.add(webServiceNoServices);
1900 pasteMenu.add(pasteNew);
1901 pasteMenu.add(pasteThis);
1902 sort.add(sortIDMenuItem);
1903 sort.add(sortLengthMenuItem);
1904 sort.add(sortGroupMenuItem);
1905 sort.add(sortPairwiseMenuItem);
1906 sort.add(sortByTreeMenu);
1907 calculateTree.add(averageDistanceTreeMenuItem);
1908 calculateTree.add(neighbourTreeMenuItem);
1909 calculateTree.add(avDistanceTreeBlosumMenuItem);
1910 calculateTree.add(njTreeBlosumMenuItem);
1911 jMenu2.add(htmlMenuItem);
1912 jMenu2.add(epsFile);
1913 jMenu2.add(createPNG);
1914 addSequenceMenu.add(addFromFile);
1915 addSequenceMenu.add(addFromText);
1916 addSequenceMenu.add(addFromURL);
1917 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1918 statusPanel.add(statusBar, null);
1919 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1920 jMenu3.add(showAllColumns);
1921 jMenu3.add(showAllSeqs);
1922 jMenu3.add(showAllhidden);
1923 hideMenu.add(hideSelColumns);
1924 hideMenu.add(hideSelSequences);
1925 hideMenu.add(hideAllSelection);
1926 hideMenu.add(hideAllButSelection);
1928 formatMenu.add(font);
1929 formatMenu.addSeparator();
1930 formatMenu.add(wrapMenuItem);
1931 formatMenu.add(scaleAbove);
1932 formatMenu.add(scaleLeft);
1933 formatMenu.add(scaleRight);
1934 formatMenu.add(seqLimits);
1935 formatMenu.add(idRightAlign);
1936 formatMenu.add(hiddenMarkers);
1937 formatMenu.add(viewBoxesMenuItem);
1938 formatMenu.add(viewTextMenuItem);
1939 formatMenu.add(colourTextMenuItem);
1940 formatMenu.add(renderGapsMenuItem);
1941 formatMenu.add(centreColumnLabelsMenuItem);
1942 formatMenu.add(showNonconservedMenuItem);
1943 selectMenu.add(findMenuItem);
1944 selectMenu.addSeparator();
1945 selectMenu.add(selectAllSequenceMenuItem);
1946 selectMenu.add(deselectAllSequenceMenuItem);
1947 selectMenu.add(invertSequenceMenuItem);
1948 selectMenu.add(invertColSel);
1949 selectMenu.add(deleteGroups);
1950 selectMenu.add(grpsFromSelection);
1951 // TODO - determine if the listenToViewSelections button is needed : see bug
1953 // selectMenu.addSeparator();
1954 // selectMenu.add(listenToViewSelections);
1957 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1959 // TODO Auto-generated method stub
1963 protected void listenToViewSelections_actionPerformed(ActionEvent e)
1965 // TODO Auto-generated method stub
1969 protected void showAllhidden_actionPerformed(ActionEvent e)
1971 // TODO Auto-generated method stub
1975 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1977 // TODO Auto-generated method stub
1981 protected void hideAllSelection_actionPerformed(ActionEvent e)
1983 // TODO Auto-generated method stub
1987 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1989 // TODO Auto-generated method stub
1993 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1995 // TODO Auto-generated method stub
1999 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2001 // TODO Auto-generated method stub
2005 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2007 // TODO Auto-generated method stub
2011 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2013 // TODO Auto-generated method stub
2017 protected void showGroupConservation_actionPerformed(ActionEvent e)
2019 // TODO Auto-generated method stub
2023 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2025 // TODO Auto-generated method stub
2029 protected void showSeqFeaturesHeight_actionPerformed(
2030 ActionEvent actionEvent)
2032 // TODO Auto-generated method stub
2036 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2038 // TODO Auto-generated method stub
2042 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2044 // TODO Auto-generated method stub
2048 protected void followHighlight_actionPerformed()
2050 // TODO Auto-generated method stub
2054 protected void showNpFeats_actionPerformed(ActionEvent e)
2056 // TODO Auto-generated method stub
2060 protected void showDbRefs_actionPerformed(ActionEvent e)
2062 // TODO Auto-generated method stub
2066 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2070 protected void showProducts_actionPerformed(ActionEvent e)
2074 protected void buildSortByAnnotationScoresMenu()
2078 protected void extractScores_actionPerformed(ActionEvent e)
2082 protected void outputText_actionPerformed(ActionEvent e)
2086 public void addFromFile_actionPerformed(ActionEvent e)
2091 public void addFromText_actionPerformed(ActionEvent e)
2096 public void addFromURL_actionPerformed(ActionEvent e)
2101 public void exportFeatures_actionPerformed(ActionEvent e)
2106 public void exportAnnotations_actionPerformed(ActionEvent e)
2111 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2115 protected void closeMenuItem_actionPerformed(boolean b)
2119 protected void redoMenuItem_actionPerformed(ActionEvent e)
2123 protected void undoMenuItem_actionPerformed(ActionEvent e)
2127 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2131 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2135 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2139 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2143 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2147 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2151 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2155 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2159 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2163 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2167 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2171 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2175 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2179 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2183 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2187 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2191 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2195 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2199 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2203 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2207 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2211 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2215 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2219 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2223 protected void clustalColour_actionPerformed(ActionEvent e)
2227 protected void zappoColour_actionPerformed(ActionEvent e)
2231 protected void taylorColour_actionPerformed(ActionEvent e)
2235 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2239 protected void helixColour_actionPerformed(ActionEvent e)
2243 protected void strandColour_actionPerformed(ActionEvent e)
2247 protected void turnColour_actionPerformed(ActionEvent e)
2251 protected void buriedColour_actionPerformed(ActionEvent e)
2255 protected void userDefinedColour_actionPerformed(ActionEvent e)
2259 protected void PIDColour_actionPerformed(ActionEvent e)
2263 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2267 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2272 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2275 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2279 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2283 protected void printMenuItem_actionPerformed(ActionEvent e)
2287 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2291 protected void findMenuItem_actionPerformed(ActionEvent e)
2295 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2299 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2303 protected void nucleotideColour_actionPerformed(ActionEvent e)
2307 protected void deleteGroups_actionPerformed(ActionEvent e)
2311 protected void copy_actionPerformed(ActionEvent e)
2315 protected void cut_actionPerformed(ActionEvent e)
2319 protected void delete_actionPerformed(ActionEvent e)
2323 protected void pasteNew_actionPerformed(ActionEvent e)
2327 protected void pasteThis_actionPerformed(ActionEvent e)
2331 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2335 public void createPNG(java.io.File f)
2339 protected void font_actionPerformed(ActionEvent e)
2343 protected void seqLimit_actionPerformed(ActionEvent e)
2347 public void seqDBRef_actionPerformed(ActionEvent e)
2352 public void createEPS(java.io.File f)
2356 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2362 * Template method to handle the 'load T-Coffee scores' menu event.
2364 * Subclasses override this method to provide a custom action.
2369 protected void loadScores_actionPerformed(ActionEvent event)
2375 * Template method to handle the 'Color T-Coffee scores' menu event.
2377 * Subclasses override this method to provide a custom action.
2382 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2387 protected void jpred_actionPerformed(ActionEvent e)
2391 protected void scaleAbove_actionPerformed(ActionEvent e)
2395 protected void scaleLeft_actionPerformed(ActionEvent e)
2399 protected void scaleRight_actionPerformed(ActionEvent e)
2403 protected void modifyPID_actionPerformed(ActionEvent e)
2407 protected void modifyConservation_actionPerformed(ActionEvent e)
2411 protected void saveAs_actionPerformed(ActionEvent e)
2415 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2419 public void vamsasStore_actionPerformed(ActionEvent e)
2424 public void vamsasLoad_actionPerformed(ActionEvent e)
2429 public void showTranslation_actionPerformed(ActionEvent e)
2434 public void featureSettings_actionPerformed(ActionEvent e)
2439 public void fetchSequence_actionPerformed(ActionEvent e)
2444 public void smoothFont_actionPerformed(ActionEvent e)
2449 public void annotationColour_actionPerformed(ActionEvent e)
2454 public void rnahelicesColour_actionPerformed(ActionEvent e)
2459 public void associatedData_actionPerformed(ActionEvent e)
2464 public void autoCalculate_actionPerformed(ActionEvent e)
2469 public void sortByTreeOption_actionPerformed(ActionEvent e)
2474 public void showAllSeqs_actionPerformed(ActionEvent e)
2479 public void showAllColumns_actionPerformed(ActionEvent e)
2484 public void hideSelSequences_actionPerformed(ActionEvent e)
2489 public void hideSelColumns_actionPerformed(ActionEvent e)
2494 public void hiddenMarkers_actionPerformed(ActionEvent e)
2499 public void findPdbId_actionPerformed(ActionEvent e)
2504 public void enterPdbId_actionPerformed(ActionEvent e)
2509 public void pdbFile_actionPerformed(ActionEvent e)
2514 public void invertColSel_actionPerformed(ActionEvent e)
2519 public void tabSelectionChanged(int sel)
2524 public void tabbedPane_mousePressed(MouseEvent e)
2529 public void tabbedPane_focusGained(FocusEvent e)
2534 public void save_actionPerformed(ActionEvent e)
2539 public void reload_actionPerformed(ActionEvent e)
2544 public void newView_actionPerformed(ActionEvent e)
2549 public void textColour_actionPerformed(ActionEvent e)
2554 public void idRightAlign_actionPerformed(ActionEvent e)
2559 public void expandViews_actionPerformed(ActionEvent e)
2564 public void gatherViews_actionPerformed(ActionEvent e)
2569 public void buildTreeMenu()
2574 public void pageSetup_actionPerformed(ActionEvent e)
2579 public void alignmentProperties()