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;
21 import jalview.util.MessageManager;
23 import java.awt.BorderLayout;
24 import java.awt.Color;
25 import java.awt.GridLayout;
26 import java.awt.Toolkit;
27 import java.awt.event.ActionEvent;
28 import java.awt.event.ActionListener;
29 import java.awt.event.FocusAdapter;
30 import java.awt.event.FocusEvent;
31 import java.awt.event.MouseAdapter;
32 import java.awt.event.MouseEvent;
34 import javax.swing.BorderFactory;
35 import javax.swing.ButtonGroup;
36 import javax.swing.JCheckBoxMenuItem;
37 import javax.swing.JInternalFrame;
38 import javax.swing.JLabel;
39 import javax.swing.JMenu;
40 import javax.swing.JMenuBar;
41 import javax.swing.JMenuItem;
42 import javax.swing.JOptionPane;
43 import javax.swing.JPanel;
44 import javax.swing.JRadioButtonMenuItem;
45 import javax.swing.JTabbedPane;
46 import javax.swing.SwingUtilities;
47 import javax.swing.event.ChangeEvent;
48 import javax.swing.event.MenuEvent;
49 import javax.swing.event.MenuListener;
51 public class GAlignFrame extends JInternalFrame
53 protected JMenuBar alignFrameMenuBar = new JMenuBar();
55 protected JMenu fileMenu = new JMenu();
57 protected JMenuItem closeMenuItem = new JMenuItem();
59 protected JMenu editMenu = new JMenu();
61 protected JMenu viewMenu = new JMenu();
63 protected JMenu colourMenu = new JMenu();
65 protected JMenu calculateMenu = new JMenu();
67 protected JMenu webService = new JMenu();
69 protected JMenuItem webServiceNoServices;
71 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
73 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
75 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
77 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
79 protected JMenuItem remove2RightMenuItem = new JMenuItem();
81 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
83 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
85 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
87 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
89 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
91 protected JMenuItem sortIDMenuItem = new JMenuItem();
93 protected JMenuItem sortLengthMenuItem = new JMenuItem();
95 protected JMenuItem sortGroupMenuItem = new JMenuItem();
97 protected JMenu sortByAnnotScore = new JMenu();
99 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
101 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
103 protected JMenuItem PCAMenuItem = new JMenuItem();
105 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
107 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
109 BorderLayout borderLayout1 = new BorderLayout();
111 public JLabel statusBar = new JLabel();
113 protected JMenuItem saveAs = new JMenuItem();
115 protected JMenu outputTextboxMenu = new JMenu();
117 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
119 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
121 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
123 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
125 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
127 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
129 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
131 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
133 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
135 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
137 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
139 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
141 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
143 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
145 // protected JRadioButtonMenuItem covariationColour = new
146 // JRadioButtonMenuItem();
148 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
150 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
152 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
154 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
156 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
158 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
160 JMenuItem htmlMenuItem = new JMenuItem();
162 JMenuItem overviewMenuItem = new JMenuItem();
164 protected JMenuItem undoMenuItem = new JMenuItem();
166 protected JMenuItem redoMenuItem = new JMenuItem();
168 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
170 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
172 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
174 JMenuItem printMenuItem = new JMenuItem();
176 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
178 JMenuItem findMenuItem = new JMenuItem();
180 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
182 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
184 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
186 JMenuItem deleteGroups = new JMenuItem();
188 JMenuItem createGroup = new JMenuItem();
189 JMenuItem unGroup = new JMenuItem();
191 JMenuItem delete = new JMenuItem();
193 JMenuItem copy = new JMenuItem();
195 JMenuItem cut = new JMenuItem();
197 JMenu pasteMenu = new JMenu();
199 JMenuItem pasteNew = new JMenuItem();
201 JMenuItem pasteThis = new JMenuItem();
203 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
205 JMenuItem createPNG = new JMenuItem();
207 protected JMenuItem font = new JMenuItem();
209 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
211 JMenuItem epsFile = new JMenuItem();
213 JMenuItem LoadtreeMenuItem = new JMenuItem();
215 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
217 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
219 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
221 protected JMenuItem modifyPID = new JMenuItem();
223 protected JMenuItem modifyConservation = new JMenuItem();
225 protected JMenu sortByTreeMenu = new JMenu();
227 protected JMenu sort = new JMenu();
229 protected JMenu calculateTree = new JMenu();
231 JMenu jMenu2 = new JMenu();
233 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
235 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
237 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
239 protected ButtonGroup colours = new ButtonGroup();
241 JMenuItem vamsasStore = new JMenuItem();
243 protected JMenuItem showTranslation = new JMenuItem();
245 protected JMenuItem extractScores = new JMenuItem();
247 protected JMenu showProducts = new JMenu();
249 public JMenuItem openFeatureSettings = new JMenuItem();
251 JMenuItem fetchSequence = new JMenuItem();
253 JMenuItem annotationColour = new JMenuItem();
255 protected JMenuItem rnahelicesColour = new JMenuItem();
257 JMenuItem associatedData = new JMenuItem();
259 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
261 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
263 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
265 JMenu addSequenceMenu = new JMenu();
267 JMenuItem addFromFile = new JMenuItem();
269 JMenuItem addFromText = new JMenuItem();
271 JMenuItem addFromURL = new JMenuItem();
273 JMenuItem exportAnnotations = new JMenuItem();
275 JMenuItem exportFeatures = new JMenuItem();
277 protected JPanel statusPanel = new JPanel();
279 GridLayout gridLayout1 = new GridLayout();
281 JMenu jMenu3 = new JMenu();
283 JMenuItem showAllSeqs = new JMenuItem();
285 JMenuItem showAllColumns = new JMenuItem();
287 JMenu hideMenu = new JMenu();
289 JMenuItem hideSelSequences = new JMenuItem();
291 JMenuItem hideSelColumns = new JMenuItem();
293 JMenuItem hideAllButSelection = new JMenuItem();
295 JMenuItem hideAllSelection = new JMenuItem();
297 JMenuItem showAllhidden = new JMenuItem();
299 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
301 JMenuItem invertColSel = new JMenuItem();
303 protected JTabbedPane tabbedPane = new JTabbedPane();
305 JMenuItem save = new JMenuItem();
307 protected JMenuItem reload = new JMenuItem();
309 JMenuItem newView = new JMenuItem();
311 JMenuItem textColour = new JMenuItem();
313 JMenu formatMenu = new JMenu();
315 JMenu selectMenu = new JMenu();
317 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
319 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
321 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
323 protected JMenuItem gatherViews = new JMenuItem();
325 protected JMenuItem expandViews = new JMenuItem();
327 JMenuItem pageSetup = new JMenuItem();
329 JMenuItem alignmentProperties = new JMenuItem();
331 JMenu tooltipSettingsMenu = new JMenu();
333 private JMenuItem justifyLeftMenuItem = new JMenuItem();
335 private JMenuItem justifyRightMenuItem = new JMenuItem();
337 JMenu autoAnnMenu = new JMenu();
339 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
341 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
343 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
345 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
347 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
349 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
351 private JMenuItem grpsFromSelection = new JMenuItem();
358 setJMenuBar(alignFrameMenuBar);
360 // dynamically fill save as menu with available formats
361 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
363 JMenuItem item = new JMenuItem(
364 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
366 item.addActionListener(new java.awt.event.ActionListener()
368 public void actionPerformed(ActionEvent e)
370 outputText_actionPerformed(e);
374 outputTextboxMenu.add(item);
376 } catch (Exception e)
380 if (!new jalview.util.Platform().isAMac())
382 closeMenuItem.setMnemonic('C');
383 outputTextboxMenu.setMnemonic('T');
384 undoMenuItem.setMnemonic('Z');
385 redoMenuItem.setMnemonic('0');
386 copy.setMnemonic('C');
387 cut.setMnemonic('U');
388 pasteMenu.setMnemonic('P');
389 reload.setMnemonic('R');
392 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
394 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
395 .getUserColourSchemes().keys();
397 while (userColours.hasMoreElements())
399 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
400 userColours.nextElement().toString());
401 radioItem.setName("USER_DEFINED");
402 radioItem.addMouseListener(new MouseAdapter()
404 public void mousePressed(MouseEvent evt)
406 if (evt.isControlDown()
407 || SwingUtilities.isRightMouseButton(evt))
409 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
411 int option = JOptionPane.showInternalConfirmDialog(
412 jalview.gui.Desktop.desktop,
413 MessageManager.getString("label.remove_from_default_list"),
414 MessageManager.getString("label.remove_user_defined_colour"),
415 JOptionPane.YES_NO_OPTION);
416 if (option == JOptionPane.YES_OPTION)
418 jalview.gui.UserDefinedColours
419 .removeColourFromDefaults(radioItem.getText());
420 colourMenu.remove(radioItem);
424 radioItem.addActionListener(new ActionListener()
426 public void actionPerformed(ActionEvent evt)
428 userDefinedColour_actionPerformed(evt);
435 radioItem.addActionListener(new ActionListener()
437 public void actionPerformed(ActionEvent evt)
439 userDefinedColour_actionPerformed(evt);
442 colourMenu.insert(radioItem, 15);
443 colours.add(radioItem);
446 colours.add(noColourmenuItem);
447 colours.add(clustalColour);
448 colours.add(zappoColour);
449 colours.add(taylorColour);
450 colours.add(hydrophobicityColour);
451 colours.add(helixColour);
452 colours.add(strandColour);
453 colours.add(turnColour);
454 colours.add(buriedColour);
455 colours.add(userDefinedColour);
456 colours.add(PIDColour);
457 colours.add(BLOSUM62Colour);
458 colours.add(nucleotideColour);
459 colours.add(purinePyrimidineColour);
460 // colours.add(covariationColour);
461 colours.add(tcoffeeColour);
462 colours.add(RNAInteractionColour);
463 setColourSelected(jalview.bin.Cache
464 .getDefault("DEFAULT_COLOUR", "None"));
468 public void setColourSelected(String defaultColour)
471 if (defaultColour != null)
473 int index = ColourSchemeProperty
474 .getColourIndexFromName(defaultColour);
478 case ColourSchemeProperty.CLUSTAL:
479 clustalColour.setSelected(true);
483 case ColourSchemeProperty.BLOSUM:
484 BLOSUM62Colour.setSelected(true);
488 case ColourSchemeProperty.PID:
489 PIDColour.setSelected(true);
493 case ColourSchemeProperty.ZAPPO:
494 zappoColour.setSelected(true);
498 case ColourSchemeProperty.TAYLOR:
499 taylorColour.setSelected(true);
502 case ColourSchemeProperty.HYDROPHOBIC:
503 hydrophobicityColour.setSelected(true);
507 case ColourSchemeProperty.HELIX:
508 helixColour.setSelected(true);
512 case ColourSchemeProperty.STRAND:
513 strandColour.setSelected(true);
517 case ColourSchemeProperty.TURN:
518 turnColour.setSelected(true);
522 case ColourSchemeProperty.BURIED:
523 buriedColour.setSelected(true);
527 case ColourSchemeProperty.NUCLEOTIDE:
528 nucleotideColour.setSelected(true);
532 case ColourSchemeProperty.TCOFFEE:
533 tcoffeeColour.setSelected(true);
536 case ColourSchemeProperty.PURINEPYRIMIDINE:
537 purinePyrimidineColour.setSelected(true);
541 case ColourSchemeProperty.RNAINTERACTION:
542 RNAInteractionColour.setSelected(true);
546 * case ColourSchemeProperty.COVARIATION:
547 * covariationColour.setSelected(true);
551 case ColourSchemeProperty.USER_DEFINED:
552 userDefinedColour.setSelected(true);
555 case ColourSchemeProperty.NONE:
557 noColourmenuItem.setSelected(true);
565 private void jbInit() throws Exception
567 fileMenu.setText("File");
568 saveAs.setText("Save As...");
569 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
570 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
571 .getMenuShortcutKeyMask()
572 | java.awt.event.KeyEvent.SHIFT_MASK, false));
573 saveAs.addActionListener(new ActionListener()
575 public void actionPerformed(ActionEvent e)
577 saveAs_actionPerformed(e);
580 closeMenuItem.setText("Close");
581 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
582 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
583 .getMenuShortcutKeyMask(), false));
584 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
586 public void actionPerformed(ActionEvent e)
588 closeMenuItem_actionPerformed(false);
591 editMenu.setText("Edit");
592 viewMenu.setText("View");
593 colourMenu.setText("Colour");
594 calculateMenu.setText("Calculate");
595 webService.setText("Web Service");
596 selectAllSequenceMenuItem.setText("Select All");
597 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
598 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
599 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
600 selectAllSequenceMenuItem
601 .addActionListener(new java.awt.event.ActionListener()
603 public void actionPerformed(ActionEvent e)
605 selectAllSequenceMenuItem_actionPerformed(e);
608 deselectAllSequenceMenuItem.setText("Deselect All");
609 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
610 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
611 deselectAllSequenceMenuItem
612 .addActionListener(new java.awt.event.ActionListener()
614 public void actionPerformed(ActionEvent e)
616 deselectAllSequenceMenuItem_actionPerformed(e);
619 invertSequenceMenuItem.setText("Invert Sequence Selection");
620 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
621 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
622 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
623 invertSequenceMenuItem
624 .addActionListener(new java.awt.event.ActionListener()
626 public void actionPerformed(ActionEvent e)
628 invertSequenceMenuItem_actionPerformed(e);
631 grpsFromSelection.setText("Make Groups For Selection");
632 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
634 public void actionPerformed(ActionEvent e)
636 makeGrpsFromSelection_actionPerformed(e);
640 remove2LeftMenuItem.setText("Remove Left");
641 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
642 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
643 .getMenuShortcutKeyMask(), false));
645 .addActionListener(new java.awt.event.ActionListener()
647 public void actionPerformed(ActionEvent e)
649 remove2LeftMenuItem_actionPerformed(e);
652 remove2RightMenuItem.setText("Remove Right");
653 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
654 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
655 .getMenuShortcutKeyMask(), false));
657 .addActionListener(new java.awt.event.ActionListener()
659 public void actionPerformed(ActionEvent e)
661 remove2RightMenuItem_actionPerformed(e);
664 removeGappedColumnMenuItem.setText("Remove Empty Columns");
665 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
666 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
667 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
668 removeGappedColumnMenuItem
669 .addActionListener(new java.awt.event.ActionListener()
671 public void actionPerformed(ActionEvent e)
673 removeGappedColumnMenuItem_actionPerformed(e);
676 removeAllGapsMenuItem.setText("Remove All Gaps");
677 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
678 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
679 .getDefaultToolkit().getMenuShortcutKeyMask()
680 | java.awt.event.KeyEvent.SHIFT_MASK, false));
681 removeAllGapsMenuItem
682 .addActionListener(new java.awt.event.ActionListener()
684 public void actionPerformed(ActionEvent e)
686 removeAllGapsMenuItem_actionPerformed(e);
689 justifyLeftMenuItem.setText("Left Justify Alignment");
691 .addActionListener(new java.awt.event.ActionListener()
693 public void actionPerformed(ActionEvent e)
695 justifyLeftMenuItem_actionPerformed(e);
698 justifyRightMenuItem.setText("Right Justify Alignment");
700 .addActionListener(new java.awt.event.ActionListener()
702 public void actionPerformed(ActionEvent e)
704 justifyRightMenuItem_actionPerformed(e);
707 viewBoxesMenuItem.setText("Boxes");
708 viewBoxesMenuItem.setState(true);
709 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
711 public void actionPerformed(ActionEvent e)
713 viewBoxesMenuItem_actionPerformed(e);
716 viewTextMenuItem.setText("Text");
717 viewTextMenuItem.setState(true);
718 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
720 public void actionPerformed(ActionEvent e)
722 viewTextMenuItem_actionPerformed(e);
725 showNonconservedMenuItem.setText("Show nonconserved");
726 showNonconservedMenuItem.setState(false);
727 showNonconservedMenuItem
728 .addActionListener(new java.awt.event.ActionListener()
730 public void actionPerformed(ActionEvent e)
732 showUnconservedMenuItem_actionPerformed(e);
735 sortPairwiseMenuItem.setText("by Pairwise Identity");
737 .addActionListener(new java.awt.event.ActionListener()
739 public void actionPerformed(ActionEvent e)
741 sortPairwiseMenuItem_actionPerformed(e);
744 sortIDMenuItem.setText("by ID");
745 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
747 public void actionPerformed(ActionEvent e)
749 sortIDMenuItem_actionPerformed(e);
752 sortLengthMenuItem.setText("By Length");
754 .addActionListener(new java.awt.event.ActionListener()
756 public void actionPerformed(ActionEvent e)
758 sortLengthMenuItem_actionPerformed(e);
761 sortGroupMenuItem.setText("by Group");
762 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
764 public void actionPerformed(ActionEvent e)
766 sortGroupMenuItem_actionPerformed(e);
769 removeRedundancyMenuItem.setText("Remove Redundancy...");
770 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
771 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
772 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
773 removeRedundancyMenuItem
774 .addActionListener(new java.awt.event.ActionListener()
776 public void actionPerformed(ActionEvent e)
778 removeRedundancyMenuItem_actionPerformed(e);
781 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
782 pairwiseAlignmentMenuItem
783 .addActionListener(new java.awt.event.ActionListener()
785 public void actionPerformed(ActionEvent e)
787 pairwiseAlignmentMenuItem_actionPerformed(e);
790 PCAMenuItem.setText("Principal Component Analysis");
791 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
793 public void actionPerformed(ActionEvent e)
795 PCAMenuItem_actionPerformed(e);
798 averageDistanceTreeMenuItem
799 .setText("Average Distance Using % Identity");
800 averageDistanceTreeMenuItem
801 .addActionListener(new java.awt.event.ActionListener()
803 public void actionPerformed(ActionEvent e)
805 averageDistanceTreeMenuItem_actionPerformed(e);
808 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
809 neighbourTreeMenuItem
810 .addActionListener(new java.awt.event.ActionListener()
812 public void actionPerformed(ActionEvent e)
814 neighbourTreeMenuItem_actionPerformed(e);
817 this.getContentPane().setLayout(borderLayout1);
818 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
819 statusBar.setBackground(Color.white);
820 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
821 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
822 statusBar.setText("Status bar");
823 outputTextboxMenu.setText("Output to Textbox");
824 clustalColour.setText("Clustalx");
826 clustalColour.addActionListener(new java.awt.event.ActionListener()
828 public void actionPerformed(ActionEvent e)
830 clustalColour_actionPerformed(e);
833 zappoColour.setText("Zappo");
834 zappoColour.addActionListener(new java.awt.event.ActionListener()
836 public void actionPerformed(ActionEvent e)
838 zappoColour_actionPerformed(e);
841 taylorColour.setText("Taylor");
842 taylorColour.addActionListener(new java.awt.event.ActionListener()
844 public void actionPerformed(ActionEvent e)
846 taylorColour_actionPerformed(e);
849 hydrophobicityColour.setText("Hydrophobicity");
851 .addActionListener(new java.awt.event.ActionListener()
853 public void actionPerformed(ActionEvent e)
855 hydrophobicityColour_actionPerformed(e);
858 helixColour.setText("Helix Propensity");
859 helixColour.addActionListener(new java.awt.event.ActionListener()
861 public void actionPerformed(ActionEvent e)
863 helixColour_actionPerformed(e);
866 strandColour.setText("Strand Propensity");
867 strandColour.addActionListener(new java.awt.event.ActionListener()
869 public void actionPerformed(ActionEvent e)
871 strandColour_actionPerformed(e);
874 turnColour.setText("Turn Propensity");
875 turnColour.addActionListener(new java.awt.event.ActionListener()
877 public void actionPerformed(ActionEvent e)
879 turnColour_actionPerformed(e);
882 buriedColour.setText("Buried Index");
883 buriedColour.addActionListener(new java.awt.event.ActionListener()
885 public void actionPerformed(ActionEvent e)
887 buriedColour_actionPerformed(e);
890 userDefinedColour.setText("User Defined...");
891 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
893 public void actionPerformed(ActionEvent e)
895 userDefinedColour_actionPerformed(e);
898 PIDColour.setText("Percentage Identity");
899 PIDColour.addActionListener(new java.awt.event.ActionListener()
901 public void actionPerformed(ActionEvent e)
903 PIDColour_actionPerformed(e);
906 BLOSUM62Colour.setText("BLOSUM62 Score");
907 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
909 public void actionPerformed(ActionEvent e)
911 BLOSUM62Colour_actionPerformed(e);
914 nucleotideColour.setText("Nucleotide");
915 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
917 public void actionPerformed(ActionEvent e)
919 nucleotideColour_actionPerformed(e);
923 purinePyrimidineColour.setText("Purine/Pyrimidine");
924 purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
926 public void actionPerformed(ActionEvent e)
928 purinePyrimidineColour_actionPerformed(e);
932 RNAInteractionColour.setText("RNA Interaction type");
933 RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
935 public void actionPerformed(ActionEvent e)
937 RNAInteractionColour_actionPerformed(e);
941 * covariationColour.setText("Covariation");
942 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
943 * public void actionPerformed(ActionEvent e) {
944 * covariationColour_actionPerformed(e); } });
947 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
948 avDistanceTreeBlosumMenuItem
949 .addActionListener(new java.awt.event.ActionListener()
951 public void actionPerformed(ActionEvent e)
953 avTreeBlosumMenuItem_actionPerformed(e);
956 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
958 .addActionListener(new java.awt.event.ActionListener()
960 public void actionPerformed(ActionEvent e)
962 njTreeBlosumMenuItem_actionPerformed(e);
965 annotationPanelMenuItem.setActionCommand("");
966 annotationPanelMenuItem.setText("Show Annotations");
967 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
968 "SHOW_ANNOTATIONS", true));
969 annotationPanelMenuItem
970 .addActionListener(new java.awt.event.ActionListener()
972 public void actionPerformed(ActionEvent e)
974 annotationPanelMenuItem_actionPerformed(e);
977 colourTextMenuItem.setText("Colour Text");
979 .addActionListener(new java.awt.event.ActionListener()
981 public void actionPerformed(ActionEvent e)
983 colourTextMenuItem_actionPerformed(e);
986 htmlMenuItem.setText("HTML");
987 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
989 public void actionPerformed(ActionEvent e)
991 htmlMenuItem_actionPerformed(e);
994 overviewMenuItem.setText("Overview Window");
995 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
997 public void actionPerformed(ActionEvent e)
999 overviewMenuItem_actionPerformed(e);
1002 undoMenuItem.setEnabled(false);
1003 undoMenuItem.setText("Undo");
1004 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1005 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1006 .getMenuShortcutKeyMask(), false));
1007 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1009 public void actionPerformed(ActionEvent e)
1011 undoMenuItem_actionPerformed(e);
1014 redoMenuItem.setEnabled(false);
1015 redoMenuItem.setText("Redo");
1016 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1017 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1018 .getMenuShortcutKeyMask(), false));
1019 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1021 public void actionPerformed(ActionEvent e)
1023 redoMenuItem_actionPerformed(e);
1026 conservationMenuItem.setText("By Conservation");
1027 conservationMenuItem
1028 .addActionListener(new java.awt.event.ActionListener()
1030 public void actionPerformed(ActionEvent e)
1032 conservationMenuItem_actionPerformed(e);
1035 noColourmenuItem.setText("None");
1036 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1038 public void actionPerformed(ActionEvent e)
1040 noColourmenuItem_actionPerformed(e);
1043 wrapMenuItem.setText("Wrap");
1044 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1046 public void actionPerformed(ActionEvent e)
1048 wrapMenuItem_actionPerformed(e);
1051 printMenuItem.setText("Print ...");
1052 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1053 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1054 .getMenuShortcutKeyMask(), false));
1055 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1057 public void actionPerformed(ActionEvent e)
1059 printMenuItem_actionPerformed(e);
1062 renderGapsMenuItem.setText("Show Gaps");
1063 renderGapsMenuItem.setState(true);
1065 .addActionListener(new java.awt.event.ActionListener()
1067 public void actionPerformed(ActionEvent e)
1069 renderGapsMenuItem_actionPerformed(e);
1072 findMenuItem.setText("Find...");
1073 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1074 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1075 .getMenuShortcutKeyMask(), false));
1076 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1078 public void actionPerformed(ActionEvent e)
1080 findMenuItem_actionPerformed(e);
1083 abovePIDThreshold.setText("Above Identity Threshold");
1084 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1086 public void actionPerformed(ActionEvent e)
1088 abovePIDThreshold_actionPerformed(e);
1091 showSeqFeatures.setText("Show Sequence Features");
1092 showSeqFeatures.addActionListener(new ActionListener()
1094 public void actionPerformed(ActionEvent actionEvent)
1096 showSeqFeatures_actionPerformed(actionEvent);
1100 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1101 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1102 * void actionPerformed(ActionEvent actionEvent) {
1103 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1105 showDbRefsMenuitem.setText("Show Database Refs");
1106 showDbRefsMenuitem.addActionListener(new ActionListener()
1109 public void actionPerformed(ActionEvent e)
1111 showDbRefs_actionPerformed(e);
1115 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1116 showNpFeatsMenuitem.addActionListener(new ActionListener()
1119 public void actionPerformed(ActionEvent e)
1121 showNpFeats_actionPerformed(e);
1125 showGroupConservation.setText("Group Conservation");
1126 showGroupConservation.addActionListener(new ActionListener()
1129 public void actionPerformed(ActionEvent e)
1131 showGroupConservation_actionPerformed(e);
1136 showGroupConsensus.setText("Group Consensus");
1137 showGroupConsensus.addActionListener(new ActionListener()
1140 public void actionPerformed(ActionEvent e)
1142 showGroupConsensus_actionPerformed(e);
1146 showConsensusHistogram.setText("Show Consensus Histogram");
1147 showConsensusHistogram.addActionListener(new ActionListener()
1150 public void actionPerformed(ActionEvent e)
1152 showConsensusHistogram_actionPerformed(e);
1156 showSequenceLogo.setText("Show Consensus Logo");
1157 showSequenceLogo.addActionListener(new ActionListener()
1160 public void actionPerformed(ActionEvent e)
1162 showSequenceLogo_actionPerformed(e);
1166 normaliseSequenceLogo.setText("Normalise Consensus Logo");
1167 normaliseSequenceLogo.addActionListener(new ActionListener()
1170 public void actionPerformed(ActionEvent e)
1172 normaliseSequenceLogo_actionPerformed(e);
1176 applyAutoAnnotationSettings.setText("Apply to all groups");
1177 applyAutoAnnotationSettings.setState(false);
1178 applyAutoAnnotationSettings.setVisible(true);
1179 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1182 public void actionPerformed(ActionEvent e)
1184 applyAutoAnnotationSettings_actionPerformed(e);
1189 nucleotideColour.setText("Nucleotide");
1190 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1192 public void actionPerformed(ActionEvent e)
1194 nucleotideColour_actionPerformed(e);
1198 tcoffeeColour.setText("T-Coffee scores");
1199 tcoffeeColour.setEnabled(false);
1200 tcoffeeColour.addActionListener(new ActionListener()
1204 public void actionPerformed(ActionEvent e)
1206 tcoffeeColorScheme_actionPerformed(e);
1210 deleteGroups.setText("Undefine groups");
1211 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1212 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1213 .getMenuShortcutKeyMask(), false));
1214 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1216 public void actionPerformed(ActionEvent e)
1218 deleteGroups_actionPerformed(e);
1221 createGroup.setText("Create group");
1222 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1223 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1224 .getMenuShortcutKeyMask(), false));
1225 createGroup.addActionListener(new java.awt.event.ActionListener()
1227 public void actionPerformed(ActionEvent e)
1229 createGroup_actionPerformed(e);
1232 unGroup.setText("Remove Group");
1233 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1234 java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
1235 .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
1236 unGroup.addActionListener(new java.awt.event.ActionListener()
1238 public void actionPerformed(ActionEvent e)
1240 unGroup_actionPerformed(e);
1243 copy.setText("Copy");
1244 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1245 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1246 .getMenuShortcutKeyMask(), false));
1248 copy.addActionListener(new java.awt.event.ActionListener()
1250 public void actionPerformed(ActionEvent e)
1252 copy_actionPerformed(e);
1256 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1257 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1258 .getMenuShortcutKeyMask(), false));
1259 cut.addActionListener(new java.awt.event.ActionListener()
1261 public void actionPerformed(ActionEvent e)
1263 cut_actionPerformed(e);
1266 delete.setText("Delete");
1267 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1268 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1269 delete.addActionListener(new java.awt.event.ActionListener()
1271 public void actionPerformed(ActionEvent e)
1273 delete_actionPerformed(e);
1276 pasteMenu.setText("Paste");
1277 pasteNew.setText("To New Alignment");
1278 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1279 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1280 .getMenuShortcutKeyMask()
1281 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1282 pasteNew.addActionListener(new java.awt.event.ActionListener()
1284 public void actionPerformed(ActionEvent e)
1286 pasteNew_actionPerformed(e);
1289 pasteThis.setText("Add To This Alignment");
1290 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1291 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1292 .getMenuShortcutKeyMask(), false));
1293 pasteThis.addActionListener(new java.awt.event.ActionListener()
1295 public void actionPerformed(ActionEvent e)
1297 pasteThis_actionPerformed(e);
1300 applyToAllGroups.setText("Apply Colour To All Groups");
1301 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1303 public void actionPerformed(ActionEvent e)
1305 applyToAllGroups_actionPerformed(e);
1308 createPNG.addActionListener(new java.awt.event.ActionListener()
1310 public void actionPerformed(ActionEvent e)
1315 createPNG.setActionCommand("Save As PNG Image");
1316 createPNG.setText("PNG");
1317 font.setText("Font...");
1318 font.addActionListener(new java.awt.event.ActionListener()
1320 public void actionPerformed(ActionEvent e)
1322 font_actionPerformed(e);
1326 seqLimits.setText("Show Sequence Limits");
1327 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1328 seqLimits.addActionListener(new java.awt.event.ActionListener()
1330 public void actionPerformed(ActionEvent e)
1332 seqLimit_actionPerformed(e);
1335 epsFile.setText("EPS");
1336 epsFile.addActionListener(new java.awt.event.ActionListener()
1338 public void actionPerformed(ActionEvent e)
1343 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1344 LoadtreeMenuItem.setText("Load Associated Tree");
1345 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1347 public void actionPerformed(ActionEvent e)
1349 LoadtreeMenuItem_actionPerformed(e);
1353 scaleAbove.setVisible(false);
1354 scaleAbove.setText("Scale Above");
1355 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1357 public void actionPerformed(ActionEvent e)
1359 scaleAbove_actionPerformed(e);
1362 scaleLeft.setVisible(false);
1363 scaleLeft.setSelected(true);
1364 scaleLeft.setText("Scale Left");
1365 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1367 public void actionPerformed(ActionEvent e)
1369 scaleLeft_actionPerformed(e);
1372 scaleRight.setVisible(false);
1373 scaleRight.setSelected(true);
1374 scaleRight.setText("Scale Right");
1375 scaleRight.addActionListener(new java.awt.event.ActionListener()
1377 public void actionPerformed(ActionEvent e)
1379 scaleRight_actionPerformed(e);
1382 centreColumnLabelsMenuItem.setVisible(true);
1383 centreColumnLabelsMenuItem.setState(false);
1384 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1385 centreColumnLabelsMenuItem
1386 .addActionListener(new java.awt.event.ActionListener()
1388 public void actionPerformed(ActionEvent e)
1390 centreColumnLabels_actionPerformed(e);
1393 followHighlightMenuItem.setVisible(true);
1394 followHighlightMenuItem.setState(true);
1395 followHighlightMenuItem.setText("Automatic Scrolling");
1396 followHighlightMenuItem.addActionListener(new ActionListener()
1399 public void actionPerformed(ActionEvent e)
1401 followHighlight_actionPerformed();
1406 modifyPID.setText("Modify Identity Threshold...");
1407 modifyPID.addActionListener(new java.awt.event.ActionListener()
1409 public void actionPerformed(ActionEvent e)
1411 modifyPID_actionPerformed(e);
1414 modifyConservation.setText("Modify Conservation Threshold...");
1416 .addActionListener(new java.awt.event.ActionListener()
1418 public void actionPerformed(ActionEvent e)
1420 modifyConservation_actionPerformed(e);
1423 sortByTreeMenu.setText("By Tree Order");
1424 sort.setText("Sort");
1425 sort.addMenuListener(new MenuListener()
1427 public void menuSelected(MenuEvent e)
1432 public void menuDeselected(MenuEvent e)
1436 public void menuCanceled(MenuEvent e)
1440 sortByAnnotScore.setText("by Score");
1441 sort.add(sortByAnnotScore);
1442 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1445 public void menuCanceled(MenuEvent e)
1449 public void menuDeselected(MenuEvent e)
1453 public void menuSelected(MenuEvent e)
1455 buildSortByAnnotationScoresMenu();
1458 sortByAnnotScore.setVisible(false);
1460 calculateTree.setText("Calculate Tree");
1462 jMenu2.setText("Export Image");
1463 padGapsMenuitem.setText("Pad Gaps");
1464 padGapsMenuitem.setState(jalview.bin.Cache
1465 .getDefault("PAD_GAPS", false));
1466 padGapsMenuitem.addActionListener(new ActionListener()
1468 public void actionPerformed(ActionEvent e)
1470 padGapsMenuitem_actionPerformed(e);
1473 vamsasStore.setVisible(false);
1474 vamsasStore.setText("VAMSAS store");
1475 vamsasStore.addActionListener(new ActionListener()
1477 public void actionPerformed(ActionEvent e)
1479 vamsasStore_actionPerformed(e);
1482 showTranslation.setText("Translate cDNA");
1483 showTranslation.addActionListener(new ActionListener()
1485 public void actionPerformed(ActionEvent e)
1487 showTranslation_actionPerformed(e);
1490 extractScores.setText("Extract Scores...");
1491 extractScores.addActionListener(new ActionListener()
1493 public void actionPerformed(ActionEvent e)
1495 extractScores_actionPerformed(e);
1498 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1500 showProducts.setText("Get Cross References");
1502 * showProducts.addActionListener(new ActionListener() {
1504 * public void actionPerformed(ActionEvent e) {
1505 * showProducts_actionPerformed(e); } });
1507 openFeatureSettings.setText("Feature Settings...");
1508 openFeatureSettings.addActionListener(new ActionListener()
1510 public void actionPerformed(ActionEvent e)
1512 featureSettings_actionPerformed(e);
1515 fetchSequence.setText("Fetch Sequence(s)...");
1516 fetchSequence.addActionListener(new ActionListener()
1518 public void actionPerformed(ActionEvent e)
1520 fetchSequence_actionPerformed(e);
1524 annotationColour.setText("By Annotation...");
1525 annotationColour.addActionListener(new ActionListener()
1527 public void actionPerformed(ActionEvent e)
1529 annotationColour_actionPerformed(e);
1533 rnahelicesColour.setText("By RNA helices");
1534 rnahelicesColour.addActionListener(new ActionListener()
1536 public void actionPerformed(ActionEvent e)
1538 rnahelicesColour_actionPerformed(e);
1542 associatedData.setText("Load Features / Annotations");
1543 associatedData.addActionListener(new ActionListener()
1545 public void actionPerformed(ActionEvent e)
1547 associatedData_actionPerformed(e);
1550 autoCalculate.setText("Autocalculate Consensus");
1551 autoCalculate.setState(jalview.bin.Cache.getDefault(
1552 "AUTO_CALC_CONSENSUS", true));
1553 autoCalculate.addActionListener(new ActionListener()
1555 public void actionPerformed(ActionEvent e)
1557 autoCalculate_actionPerformed(e);
1560 sortByTree.setText("Sort Alignment With New Tree");
1562 .setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1564 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1565 sortByTree.addActionListener(new ActionListener()
1567 public void actionPerformed(ActionEvent e)
1569 sortByTreeOption_actionPerformed(e);
1573 listenToViewSelections.setText("Listen for selections");
1574 listenToViewSelections
1575 .setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1576 listenToViewSelections.setState(false);
1577 listenToViewSelections.addActionListener(new ActionListener()
1579 public void actionPerformed(ActionEvent e)
1581 listenToViewSelections_actionPerformed(e);
1585 addSequenceMenu.setText("Add Sequences");
1586 addFromFile.setText("From File");
1587 addFromFile.addActionListener(new ActionListener()
1589 public void actionPerformed(ActionEvent e)
1591 addFromFile_actionPerformed(e);
1594 addFromText.setText("From Textbox");
1595 addFromText.addActionListener(new ActionListener()
1597 public void actionPerformed(ActionEvent e)
1599 addFromText_actionPerformed(e);
1602 addFromURL.setText("From URL");
1603 addFromURL.addActionListener(new ActionListener()
1605 public void actionPerformed(ActionEvent e)
1607 addFromURL_actionPerformed(e);
1610 exportFeatures.setText("Export Features...");
1611 exportFeatures.addActionListener(new ActionListener()
1613 public void actionPerformed(ActionEvent e)
1615 exportFeatures_actionPerformed(e);
1618 exportAnnotations.setText("Export Annotations...");
1619 exportAnnotations.addActionListener(new ActionListener()
1621 public void actionPerformed(ActionEvent e)
1623 exportAnnotations_actionPerformed(e);
1626 statusPanel.setLayout(gridLayout1);
1627 jMenu3.setText("Show");
1628 showAllSeqs.setText("All Sequences");
1629 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1630 showAllSeqs.addActionListener(new ActionListener()
1632 public void actionPerformed(ActionEvent e)
1634 showAllSeqs_actionPerformed(e);
1637 showAllColumns.setText("All Columns");
1638 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1639 showAllColumns.addActionListener(new ActionListener()
1641 public void actionPerformed(ActionEvent e)
1643 showAllColumns_actionPerformed(e);
1646 hideMenu.setText("Hide");
1647 hideSelSequences.setText("Selected Sequences");
1648 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1649 hideSelSequences.addActionListener(new ActionListener()
1651 public void actionPerformed(ActionEvent e)
1653 hideSelSequences_actionPerformed(e);
1656 hideSelColumns.setText("Selected Columns");
1657 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1658 hideSelColumns.addActionListener(new ActionListener()
1660 public void actionPerformed(ActionEvent e)
1662 hideSelColumns_actionPerformed(e);
1665 hideAllSelection.setText("Selected Region");
1666 hideAllSelection.addActionListener(new ActionListener()
1668 public void actionPerformed(ActionEvent e)
1670 hideAllSelection_actionPerformed(e);
1673 // TODO: should be hidden if no selection exists.
1674 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1675 hideAllButSelection.addActionListener(new ActionListener()
1677 public void actionPerformed(ActionEvent e)
1679 hideAllButSelection_actionPerformed(e);
1682 showAllhidden.setText("All Sequences and Columns");
1684 .setToolTipText("H toggles visibility of hidden or selected regions.");
1685 showAllhidden.addActionListener(new ActionListener()
1687 public void actionPerformed(ActionEvent e)
1689 showAllhidden_actionPerformed(e);
1693 hiddenMarkers.setText("Show Hidden Markers");
1694 hiddenMarkers.addActionListener(new ActionListener()
1696 public void actionPerformed(ActionEvent e)
1698 hiddenMarkers_actionPerformed(e);
1701 invertColSel.setText("Invert Column Selection");
1702 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1703 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1704 .getMenuShortcutKeyMask()
1705 | java.awt.event.KeyEvent.ALT_MASK, false));
1706 invertColSel.addActionListener(new ActionListener()
1708 public void actionPerformed(ActionEvent e)
1710 invertColSel_actionPerformed(e);
1713 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1715 public void stateChanged(ChangeEvent evt)
1717 JTabbedPane pane = (JTabbedPane) evt.getSource();
1718 int sel = pane.getSelectedIndex();
1719 tabSelectionChanged(sel);
1722 tabbedPane.addMouseListener(new MouseAdapter()
1724 public void mousePressed(MouseEvent e)
1726 tabbedPane_mousePressed(e);
1729 tabbedPane.addFocusListener(new FocusAdapter()
1731 public void focusGained(FocusEvent e)
1733 tabbedPane_focusGained(e);
1736 save.setText("Save");
1737 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1738 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1739 .getMenuShortcutKeyMask(), false));
1740 save.addActionListener(new ActionListener()
1742 public void actionPerformed(ActionEvent e)
1744 save_actionPerformed(e);
1747 reload.setEnabled(false);
1748 reload.setText("Reload");
1749 reload.addActionListener(new ActionListener()
1751 public void actionPerformed(ActionEvent e)
1753 reload_actionPerformed(e);
1756 newView.setText("New View");
1757 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1758 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1759 .getMenuShortcutKeyMask(), false));
1760 newView.addActionListener(new ActionListener()
1762 public void actionPerformed(ActionEvent e)
1764 newView_actionPerformed(e);
1767 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1768 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1769 textColour.setText("Colour Text ...");
1770 textColour.addActionListener(new ActionListener()
1772 public void actionPerformed(ActionEvent e)
1774 textColour_actionPerformed(e);
1777 formatMenu.setText("Format");
1778 selectMenu.setText("Select");
1779 idRightAlign.setText("Right Align Sequence Id");
1780 idRightAlign.addActionListener(new ActionListener()
1782 public void actionPerformed(ActionEvent e)
1784 idRightAlign_actionPerformed(e);
1787 gatherViews.setEnabled(false);
1788 gatherViews.setText("Gather Views");
1789 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1790 java.awt.event.KeyEvent.VK_G, 0, false));
1791 gatherViews.addActionListener(new ActionListener()
1793 public void actionPerformed(ActionEvent e)
1795 gatherViews_actionPerformed(e);
1798 expandViews.setEnabled(false);
1799 expandViews.setText("Expand Views");
1800 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1801 java.awt.event.KeyEvent.VK_X, 0, false));
1802 expandViews.addActionListener(new ActionListener()
1804 public void actionPerformed(ActionEvent e)
1806 expandViews_actionPerformed(e);
1809 pageSetup.setText("Page Setup ...");
1810 pageSetup.addActionListener(new ActionListener()
1812 public void actionPerformed(ActionEvent e)
1814 pageSetup_actionPerformed(e);
1817 alignmentProperties.setText("Alignment Properties...");
1818 alignmentProperties.addActionListener(new ActionListener()
1820 public void actionPerformed(ActionEvent actionEvent)
1822 alignmentProperties();
1825 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1826 autoAnnMenu.setText("Autocalculated Annotation");
1827 alignFrameMenuBar.add(fileMenu);
1828 alignFrameMenuBar.add(editMenu);
1829 alignFrameMenuBar.add(selectMenu);
1830 alignFrameMenuBar.add(viewMenu);
1831 alignFrameMenuBar.add(formatMenu);
1832 alignFrameMenuBar.add(colourMenu);
1833 alignFrameMenuBar.add(calculateMenu);
1834 alignFrameMenuBar.add(webService);
1835 fileMenu.add(fetchSequence);
1836 fileMenu.add(addSequenceMenu);
1837 fileMenu.add(reload);
1838 fileMenu.addSeparator();
1839 fileMenu.add(vamsasStore);
1841 fileMenu.add(saveAs);
1842 fileMenu.add(outputTextboxMenu);
1843 fileMenu.add(pageSetup);
1844 fileMenu.add(printMenuItem);
1845 fileMenu.addSeparator();
1846 fileMenu.add(jMenu2);
1847 fileMenu.add(exportFeatures);
1848 fileMenu.add(exportAnnotations);
1849 fileMenu.add(LoadtreeMenuItem);
1850 fileMenu.add(associatedData);
1851 fileMenu.addSeparator();
1852 fileMenu.add(closeMenuItem);
1853 editMenu.add(undoMenuItem);
1854 editMenu.add(redoMenuItem);
1857 editMenu.add(pasteMenu);
1858 editMenu.add(delete);
1859 editMenu.addSeparator();
1860 editMenu.add(remove2LeftMenuItem);
1861 editMenu.add(remove2RightMenuItem);
1862 editMenu.add(removeGappedColumnMenuItem);
1863 editMenu.add(removeAllGapsMenuItem);
1864 editMenu.add(removeRedundancyMenuItem);
1865 editMenu.addSeparator();
1866 // dont add these yet in the CVS build - they cannot be undone!
1867 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1868 // editMenu.add(justifyLeftMenuItem);
1869 // editMenu.add(justifyRightMenuItem);
1870 // editMenu.addSeparator();
1871 editMenu.add(padGapsMenuitem);
1872 viewMenu.add(newView);
1873 viewMenu.add(expandViews);
1874 viewMenu.add(gatherViews);
1875 viewMenu.addSeparator();
1876 viewMenu.add(jMenu3);
1877 viewMenu.add(hideMenu);
1878 viewMenu.addSeparator();
1879 viewMenu.add(followHighlightMenuItem);
1880 viewMenu.add(annotationPanelMenuItem);
1881 autoAnnMenu.add(applyAutoAnnotationSettings);
1882 autoAnnMenu.add(showConsensusHistogram);
1883 autoAnnMenu.add(showSequenceLogo);
1884 autoAnnMenu.add(normaliseSequenceLogo);
1885 autoAnnMenu.addSeparator();
1886 autoAnnMenu.add(showGroupConservation);
1887 autoAnnMenu.add(showGroupConsensus);
1888 viewMenu.add(autoAnnMenu);
1889 viewMenu.addSeparator();
1890 viewMenu.add(showSeqFeatures);
1891 // viewMenu.add(showSeqFeaturesHeight);
1893 viewMenu.add(openFeatureSettings);
1894 tooltipSettingsMenu.add(showDbRefsMenuitem);
1895 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1896 viewMenu.add(tooltipSettingsMenu);
1897 viewMenu.addSeparator();
1898 viewMenu.add(alignmentProperties);
1899 viewMenu.addSeparator();
1900 viewMenu.add(overviewMenuItem);
1901 colourMenu.add(applyToAllGroups);
1902 colourMenu.add(textColour);
1903 colourMenu.addSeparator();
1904 colourMenu.add(noColourmenuItem);
1905 colourMenu.add(clustalColour);
1906 colourMenu.add(BLOSUM62Colour);
1907 colourMenu.add(PIDColour);
1908 colourMenu.add(zappoColour);
1909 colourMenu.add(taylorColour);
1910 colourMenu.add(hydrophobicityColour);
1911 colourMenu.add(helixColour);
1912 colourMenu.add(strandColour);
1913 colourMenu.add(turnColour);
1914 colourMenu.add(buriedColour);
1915 colourMenu.add(nucleotideColour);
1916 colourMenu.add(purinePyrimidineColour);
1917 colourMenu.add(RNAInteractionColour);
1918 // colourMenu.add(covariationColour);
1919 colourMenu.add(tcoffeeColour);
1920 colourMenu.add(userDefinedColour);
1921 colourMenu.addSeparator();
1922 colourMenu.add(conservationMenuItem);
1923 colourMenu.add(modifyConservation);
1924 colourMenu.add(abovePIDThreshold);
1925 colourMenu.add(modifyPID);
1926 colourMenu.add(annotationColour);
1927 colourMenu.add(rnahelicesColour);
1928 calculateMenu.add(sort);
1929 calculateMenu.add(calculateTree);
1930 calculateMenu.addSeparator();
1931 calculateMenu.add(pairwiseAlignmentMenuItem);
1932 calculateMenu.add(PCAMenuItem);
1933 calculateMenu.addSeparator();
1934 calculateMenu.add(showTranslation);
1935 calculateMenu.add(showProducts);
1936 calculateMenu.add(autoCalculate);
1937 calculateMenu.add(sortByTree);
1938 calculateMenu.addSeparator();
1939 calculateMenu.add(extractScores);
1940 webServiceNoServices = new JMenuItem("<No Services>");
1941 webService.add(webServiceNoServices);
1942 pasteMenu.add(pasteNew);
1943 pasteMenu.add(pasteThis);
1944 sort.add(sortIDMenuItem);
1945 sort.add(sortLengthMenuItem);
1946 sort.add(sortGroupMenuItem);
1947 sort.add(sortPairwiseMenuItem);
1948 sort.add(sortByTreeMenu);
1949 calculateTree.add(averageDistanceTreeMenuItem);
1950 calculateTree.add(neighbourTreeMenuItem);
1951 calculateTree.add(avDistanceTreeBlosumMenuItem);
1952 calculateTree.add(njTreeBlosumMenuItem);
1953 jMenu2.add(htmlMenuItem);
1954 jMenu2.add(epsFile);
1955 jMenu2.add(createPNG);
1956 addSequenceMenu.add(addFromFile);
1957 addSequenceMenu.add(addFromText);
1958 addSequenceMenu.add(addFromURL);
1959 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1960 statusPanel.add(statusBar, null);
1961 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1962 jMenu3.add(showAllColumns);
1963 jMenu3.add(showAllSeqs);
1964 jMenu3.add(showAllhidden);
1965 hideMenu.add(hideSelColumns);
1966 hideMenu.add(hideSelSequences);
1967 hideMenu.add(hideAllSelection);
1968 hideMenu.add(hideAllButSelection);
1970 formatMenu.add(font);
1971 formatMenu.addSeparator();
1972 formatMenu.add(wrapMenuItem);
1973 formatMenu.add(scaleAbove);
1974 formatMenu.add(scaleLeft);
1975 formatMenu.add(scaleRight);
1976 formatMenu.add(seqLimits);
1977 formatMenu.add(idRightAlign);
1978 formatMenu.add(hiddenMarkers);
1979 formatMenu.add(viewBoxesMenuItem);
1980 formatMenu.add(viewTextMenuItem);
1981 formatMenu.add(colourTextMenuItem);
1982 formatMenu.add(renderGapsMenuItem);
1983 formatMenu.add(centreColumnLabelsMenuItem);
1984 formatMenu.add(showNonconservedMenuItem);
1985 selectMenu.add(findMenuItem);
1986 selectMenu.addSeparator();
1987 selectMenu.add(selectAllSequenceMenuItem);
1988 selectMenu.add(deselectAllSequenceMenuItem);
1989 selectMenu.add(invertSequenceMenuItem);
1990 selectMenu.add(invertColSel);
1991 selectMenu.add(createGroup);
1992 selectMenu.add(unGroup);
1993 selectMenu.add(grpsFromSelection);
1994 selectMenu.add(deleteGroups);
1995 // TODO - determine if the listenToViewSelections button is needed : see bug
1997 // selectMenu.addSeparator();
1998 // selectMenu.add(listenToViewSelections);
2001 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2003 // TODO Auto-generated method stub
2007 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2009 // TODO Auto-generated method stub
2013 protected void showAllhidden_actionPerformed(ActionEvent e)
2015 // TODO Auto-generated method stub
2019 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2021 // TODO Auto-generated method stub
2025 protected void hideAllSelection_actionPerformed(ActionEvent e)
2027 // TODO Auto-generated method stub
2031 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2033 // TODO Auto-generated method stub
2037 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2039 // TODO Auto-generated method stub
2043 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2045 // TODO Auto-generated method stub
2049 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2051 // TODO Auto-generated method stub
2055 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2057 // TODO Auto-generated method stub
2061 protected void showGroupConservation_actionPerformed(ActionEvent e)
2063 // TODO Auto-generated method stub
2067 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2069 // TODO Auto-generated method stub
2073 protected void showSeqFeaturesHeight_actionPerformed(
2074 ActionEvent actionEvent)
2076 // TODO Auto-generated method stub
2080 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2082 // TODO Auto-generated method stub
2086 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2088 // TODO Auto-generated method stub
2092 protected void followHighlight_actionPerformed()
2094 // TODO Auto-generated method stub
2098 protected void showNpFeats_actionPerformed(ActionEvent e)
2100 // TODO Auto-generated method stub
2104 protected void showDbRefs_actionPerformed(ActionEvent e)
2106 // TODO Auto-generated method stub
2110 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2114 protected void showProducts_actionPerformed(ActionEvent e)
2118 protected void buildSortByAnnotationScoresMenu()
2122 protected void extractScores_actionPerformed(ActionEvent e)
2126 protected void outputText_actionPerformed(ActionEvent e)
2130 public void addFromFile_actionPerformed(ActionEvent e)
2135 public void addFromText_actionPerformed(ActionEvent e)
2140 public void addFromURL_actionPerformed(ActionEvent e)
2145 public void exportFeatures_actionPerformed(ActionEvent e)
2150 public void exportAnnotations_actionPerformed(ActionEvent e)
2155 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2159 protected void closeMenuItem_actionPerformed(boolean b)
2163 protected void redoMenuItem_actionPerformed(ActionEvent e)
2167 protected void undoMenuItem_actionPerformed(ActionEvent e)
2171 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2175 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2179 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2183 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2187 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2191 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2195 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2199 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2203 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2207 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2211 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2215 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2219 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2223 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2227 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2231 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2235 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2239 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2243 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2247 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2251 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2255 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2259 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2263 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2267 protected void clustalColour_actionPerformed(ActionEvent e)
2271 protected void zappoColour_actionPerformed(ActionEvent e)
2275 protected void taylorColour_actionPerformed(ActionEvent e)
2279 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2283 protected void helixColour_actionPerformed(ActionEvent e)
2287 protected void strandColour_actionPerformed(ActionEvent e)
2291 protected void turnColour_actionPerformed(ActionEvent e)
2295 protected void buriedColour_actionPerformed(ActionEvent e)
2299 protected void userDefinedColour_actionPerformed(ActionEvent e)
2303 protected void PIDColour_actionPerformed(ActionEvent e)
2307 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2311 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2315 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2321 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2324 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2328 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2332 protected void printMenuItem_actionPerformed(ActionEvent e)
2336 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2340 protected void findMenuItem_actionPerformed(ActionEvent e)
2344 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2348 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2352 protected void nucleotideColour_actionPerformed(ActionEvent e)
2356 protected void deleteGroups_actionPerformed(ActionEvent e)
2360 protected void createGroup_actionPerformed(ActionEvent e)
2364 protected void unGroup_actionPerformed(ActionEvent e)
2368 protected void copy_actionPerformed(ActionEvent e)
2372 protected void cut_actionPerformed(ActionEvent e)
2376 protected void delete_actionPerformed(ActionEvent e)
2380 protected void pasteNew_actionPerformed(ActionEvent e)
2384 protected void pasteThis_actionPerformed(ActionEvent e)
2388 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2392 public void createPNG(java.io.File f)
2396 protected void font_actionPerformed(ActionEvent e)
2400 protected void seqLimit_actionPerformed(ActionEvent e)
2404 public void seqDBRef_actionPerformed(ActionEvent e)
2409 public void createEPS(java.io.File f)
2413 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2419 * Template method to handle the 'load T-Coffee scores' menu event.
2421 * Subclasses override this method to provide a custom action.
2426 protected void loadScores_actionPerformed(ActionEvent event)
2432 * Template method to handle the 'Color T-Coffee scores' menu event.
2434 * Subclasses override this method to provide a custom action.
2439 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2444 protected void jpred_actionPerformed(ActionEvent e)
2448 protected void scaleAbove_actionPerformed(ActionEvent e)
2452 protected void scaleLeft_actionPerformed(ActionEvent e)
2456 protected void scaleRight_actionPerformed(ActionEvent e)
2460 protected void modifyPID_actionPerformed(ActionEvent e)
2464 protected void modifyConservation_actionPerformed(ActionEvent e)
2468 protected void saveAs_actionPerformed(ActionEvent e)
2472 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2476 public void vamsasStore_actionPerformed(ActionEvent e)
2481 public void vamsasLoad_actionPerformed(ActionEvent e)
2486 public void showTranslation_actionPerformed(ActionEvent e)
2491 public void featureSettings_actionPerformed(ActionEvent e)
2496 public void fetchSequence_actionPerformed(ActionEvent e)
2501 public void smoothFont_actionPerformed(ActionEvent e)
2506 public void annotationColour_actionPerformed(ActionEvent e)
2511 public void rnahelicesColour_actionPerformed(ActionEvent e)
2516 public void associatedData_actionPerformed(ActionEvent e)
2521 public void autoCalculate_actionPerformed(ActionEvent e)
2526 public void sortByTreeOption_actionPerformed(ActionEvent e)
2531 public void showAllSeqs_actionPerformed(ActionEvent e)
2536 public void showAllColumns_actionPerformed(ActionEvent e)
2541 public void hideSelSequences_actionPerformed(ActionEvent e)
2546 public void hideSelColumns_actionPerformed(ActionEvent e)
2551 public void hiddenMarkers_actionPerformed(ActionEvent e)
2556 public void findPdbId_actionPerformed(ActionEvent e)
2561 public void enterPdbId_actionPerformed(ActionEvent e)
2566 public void pdbFile_actionPerformed(ActionEvent e)
2571 public void invertColSel_actionPerformed(ActionEvent e)
2576 public void tabSelectionChanged(int sel)
2581 public void tabbedPane_mousePressed(MouseEvent e)
2586 public void tabbedPane_focusGained(FocusEvent e)
2591 public void save_actionPerformed(ActionEvent e)
2596 public void reload_actionPerformed(ActionEvent e)
2601 public void newView_actionPerformed(ActionEvent e)
2606 public void textColour_actionPerformed(ActionEvent e)
2611 public void idRightAlign_actionPerformed(ActionEvent e)
2616 public void expandViews_actionPerformed(ActionEvent e)
2621 public void gatherViews_actionPerformed(ActionEvent e)
2626 public void buildTreeMenu()
2631 public void pageSetup_actionPerformed(ActionEvent e)
2636 public void alignmentProperties()