2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.jbgui;
20 import jalview.schemes.ColourSchemeProperty;
22 import java.awt.BorderLayout;
23 import java.awt.Color;
24 import java.awt.GridLayout;
25 import java.awt.Toolkit;
26 import java.awt.event.ActionEvent;
27 import java.awt.event.ActionListener;
28 import java.awt.event.FocusAdapter;
29 import java.awt.event.FocusEvent;
30 import java.awt.event.MouseAdapter;
31 import java.awt.event.MouseEvent;
33 import javax.swing.BorderFactory;
34 import javax.swing.ButtonGroup;
35 import javax.swing.JCheckBoxMenuItem;
36 import javax.swing.JInternalFrame;
37 import javax.swing.JLabel;
38 import javax.swing.JMenu;
39 import javax.swing.JMenuBar;
40 import javax.swing.JMenuItem;
41 import javax.swing.JOptionPane;
42 import javax.swing.JPanel;
43 import javax.swing.JRadioButtonMenuItem;
44 import javax.swing.JTabbedPane;
45 import javax.swing.SwingUtilities;
46 import javax.swing.event.ChangeEvent;
47 import javax.swing.event.MenuEvent;
48 import javax.swing.event.MenuListener;
50 public class GAlignFrame extends JInternalFrame
52 protected JMenuBar alignFrameMenuBar = new JMenuBar();
54 protected JMenu fileMenu = new JMenu();
56 protected JMenuItem closeMenuItem = new JMenuItem();
58 protected JMenu editMenu = new JMenu();
60 protected JMenu viewMenu = new JMenu();
62 protected JMenu colourMenu = new JMenu();
64 protected JMenu calculateMenu = new JMenu();
66 protected JMenu webService = new JMenu();
68 protected JMenuItem webServiceNoServices;
70 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
72 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
74 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
76 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
78 protected JMenuItem remove2RightMenuItem = new JMenuItem();
80 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
82 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
84 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
86 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
88 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
90 protected JMenuItem sortIDMenuItem = new JMenuItem();
92 protected JMenuItem sortLengthMenuItem = new JMenuItem();
94 protected JMenuItem sortGroupMenuItem = new JMenuItem();
96 protected JMenu sortByAnnotScore = new JMenu();
98 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
100 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
102 protected JMenuItem PCAMenuItem = new JMenuItem();
104 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
106 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
108 BorderLayout borderLayout1 = new BorderLayout();
110 public JLabel statusBar = new JLabel();
112 protected JMenuItem saveAs = new JMenuItem();
114 protected JMenu outputTextboxMenu = new JMenu();
116 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
118 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
120 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
122 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
124 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
126 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
128 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
130 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
132 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
134 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
136 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
138 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
140 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
142 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
144 // protected JRadioButtonMenuItem covariationColour = new
145 // JRadioButtonMenuItem();
147 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 delete = new JMenuItem();
190 JMenuItem copy = new JMenuItem();
192 JMenuItem cut = new JMenuItem();
194 JMenu pasteMenu = new JMenu();
196 JMenuItem pasteNew = new JMenuItem();
198 JMenuItem pasteThis = new JMenuItem();
200 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
202 JMenuItem createPNG = new JMenuItem();
204 protected JMenuItem font = new JMenuItem();
206 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
208 JMenuItem epsFile = new JMenuItem();
210 JMenuItem LoadtreeMenuItem = new JMenuItem();
212 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
214 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
216 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
218 protected JMenuItem modifyPID = new JMenuItem();
220 protected JMenuItem modifyConservation = new JMenuItem();
222 protected JMenu sortByTreeMenu = new JMenu();
224 protected JMenu sort = new JMenu();
226 protected JMenu calculateTree = new JMenu();
228 JMenu jMenu2 = new JMenu();
230 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
232 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
234 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
236 protected ButtonGroup colours = new ButtonGroup();
238 JMenuItem vamsasStore = new JMenuItem();
240 protected JMenuItem showTranslation = new JMenuItem();
242 protected JMenuItem extractScores = new JMenuItem();
244 protected JMenu showProducts = new JMenu();
246 public JMenuItem openFeatureSettings = new JMenuItem();
248 JMenuItem fetchSequence = new JMenuItem();
250 JMenuItem annotationColour = new JMenuItem();
252 protected JMenuItem rnahelicesColour = new JMenuItem();
254 JMenuItem associatedData = new JMenuItem();
256 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
258 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
260 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
262 JMenu addSequenceMenu = new JMenu();
264 JMenuItem addFromFile = new JMenuItem();
266 JMenuItem addFromText = new JMenuItem();
268 JMenuItem addFromURL = new JMenuItem();
270 JMenuItem exportAnnotations = new JMenuItem();
272 JMenuItem exportFeatures = new JMenuItem();
274 protected JPanel statusPanel = new JPanel();
276 GridLayout gridLayout1 = new GridLayout();
278 JMenu jMenu3 = new JMenu();
280 JMenuItem showAllSeqs = new JMenuItem();
282 JMenuItem showAllColumns = new JMenuItem();
284 JMenu hideMenu = new JMenu();
286 JMenuItem hideSelSequences = new JMenuItem();
288 JMenuItem hideSelColumns = new JMenuItem();
290 JMenuItem hideAllButSelection = new JMenuItem();
292 JMenuItem hideAllSelection = new JMenuItem();
294 JMenuItem showAllhidden = new JMenuItem();
296 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
298 JMenuItem invertColSel = new JMenuItem();
300 protected JTabbedPane tabbedPane = new JTabbedPane();
302 JMenuItem save = new JMenuItem();
304 protected JMenuItem reload = new JMenuItem();
306 JMenuItem newView = new JMenuItem();
308 JMenuItem textColour = new JMenuItem();
310 JMenu formatMenu = new JMenu();
312 JMenu selectMenu = new JMenu();
314 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
316 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
318 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
320 protected JMenuItem gatherViews = new JMenuItem();
322 protected JMenuItem expandViews = new JMenuItem();
324 JMenuItem pageSetup = new JMenuItem();
326 JMenuItem alignmentProperties = new JMenuItem();
328 JMenu tooltipSettingsMenu = new JMenu();
330 private JMenuItem justifyLeftMenuItem = new JMenuItem();
332 private JMenuItem justifyRightMenuItem = new JMenuItem();
334 JMenu autoAnnMenu = new JMenu();
336 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
338 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
340 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
342 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
344 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
346 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
348 private JMenuItem grpsFromSelection = new JMenuItem();
355 setJMenuBar(alignFrameMenuBar);
357 // dynamically fill save as menu with available formats
358 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
360 JMenuItem item = new JMenuItem(
361 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
363 item.addActionListener(new java.awt.event.ActionListener()
365 public void actionPerformed(ActionEvent e)
367 outputText_actionPerformed(e);
371 outputTextboxMenu.add(item);
373 } catch (Exception e)
377 if (!new jalview.util.Platform().isAMac())
379 closeMenuItem.setMnemonic('C');
380 outputTextboxMenu.setMnemonic('T');
381 undoMenuItem.setMnemonic('Z');
382 redoMenuItem.setMnemonic('0');
383 copy.setMnemonic('C');
384 cut.setMnemonic('U');
385 pasteMenu.setMnemonic('P');
386 reload.setMnemonic('R');
389 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
391 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
392 .getUserColourSchemes().keys();
394 while (userColours.hasMoreElements())
396 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
397 userColours.nextElement().toString());
398 radioItem.setName("USER_DEFINED");
399 radioItem.addMouseListener(new MouseAdapter()
401 public void mousePressed(MouseEvent evt)
403 if (evt.isControlDown()
404 || SwingUtilities.isRightMouseButton(evt))
406 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
408 int option = JOptionPane.showInternalConfirmDialog(
409 jalview.gui.Desktop.desktop,
410 "Remove from default list?",
411 "Remove user defined colour",
412 JOptionPane.YES_NO_OPTION);
413 if (option == JOptionPane.YES_OPTION)
415 jalview.gui.UserDefinedColours
416 .removeColourFromDefaults(radioItem.getText());
417 colourMenu.remove(radioItem);
421 radioItem.addActionListener(new ActionListener()
423 public void actionPerformed(ActionEvent evt)
425 userDefinedColour_actionPerformed(evt);
432 radioItem.addActionListener(new ActionListener()
434 public void actionPerformed(ActionEvent evt)
436 userDefinedColour_actionPerformed(evt);
439 colourMenu.insert(radioItem, 15);
440 colours.add(radioItem);
443 colours.add(noColourmenuItem);
444 colours.add(clustalColour);
445 colours.add(zappoColour);
446 colours.add(taylorColour);
447 colours.add(hydrophobicityColour);
448 colours.add(helixColour);
449 colours.add(strandColour);
450 colours.add(turnColour);
451 colours.add(buriedColour);
452 colours.add(userDefinedColour);
453 colours.add(PIDColour);
454 colours.add(BLOSUM62Colour);
455 colours.add(nucleotideColour);
456 colours.add(purinePyrimidineColour);
457 // colours.add(covariationColour);
458 colours.add(tcoffeeColour);
459 colours.add(RNAInteractionColour);
460 setColourSelected(jalview.bin.Cache
461 .getDefault("DEFAULT_COLOUR", "None"));
465 public void setColourSelected(String defaultColour)
468 if (defaultColour != null)
470 int index = ColourSchemeProperty
471 .getColourIndexFromName(defaultColour);
475 case ColourSchemeProperty.CLUSTAL:
476 clustalColour.setSelected(true);
480 case ColourSchemeProperty.BLOSUM:
481 BLOSUM62Colour.setSelected(true);
485 case ColourSchemeProperty.PID:
486 PIDColour.setSelected(true);
490 case ColourSchemeProperty.ZAPPO:
491 zappoColour.setSelected(true);
495 case ColourSchemeProperty.TAYLOR:
496 taylorColour.setSelected(true);
499 case ColourSchemeProperty.HYDROPHOBIC:
500 hydrophobicityColour.setSelected(true);
504 case ColourSchemeProperty.HELIX:
505 helixColour.setSelected(true);
509 case ColourSchemeProperty.STRAND:
510 strandColour.setSelected(true);
514 case ColourSchemeProperty.TURN:
515 turnColour.setSelected(true);
519 case ColourSchemeProperty.BURIED:
520 buriedColour.setSelected(true);
524 case ColourSchemeProperty.NUCLEOTIDE:
525 nucleotideColour.setSelected(true);
529 case ColourSchemeProperty.TCOFFEE:
530 tcoffeeColour.setSelected(true);
533 case ColourSchemeProperty.PURINEPYRIMIDINE:
534 purinePyrimidineColour.setSelected(true);
538 case ColourSchemeProperty.RNAINTERACTION:
539 RNAInteractionColour.setSelected(true);
543 * case ColourSchemeProperty.COVARIATION:
544 * covariationColour.setSelected(true);
548 case ColourSchemeProperty.USER_DEFINED:
549 userDefinedColour.setSelected(true);
552 case ColourSchemeProperty.NONE:
554 noColourmenuItem.setSelected(true);
562 private void jbInit() throws Exception
564 fileMenu.setText("File");
565 saveAs.setText("Save As...");
566 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
567 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
568 .getMenuShortcutKeyMask()
569 | java.awt.event.KeyEvent.SHIFT_MASK, false));
570 saveAs.addActionListener(new ActionListener()
572 public void actionPerformed(ActionEvent e)
574 saveAs_actionPerformed(e);
577 closeMenuItem.setText("Close");
578 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
579 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
580 .getMenuShortcutKeyMask(), false));
581 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
583 public void actionPerformed(ActionEvent e)
585 closeMenuItem_actionPerformed(false);
588 editMenu.setText("Edit");
589 viewMenu.setText("View");
590 colourMenu.setText("Colour");
591 calculateMenu.setText("Calculate");
592 webService.setText("Web Service");
593 selectAllSequenceMenuItem.setText("Select All");
594 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
595 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
596 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
597 selectAllSequenceMenuItem
598 .addActionListener(new java.awt.event.ActionListener()
600 public void actionPerformed(ActionEvent e)
602 selectAllSequenceMenuItem_actionPerformed(e);
605 deselectAllSequenceMenuItem.setText("Deselect All");
606 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
607 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
608 deselectAllSequenceMenuItem
609 .addActionListener(new java.awt.event.ActionListener()
611 public void actionPerformed(ActionEvent e)
613 deselectAllSequenceMenuItem_actionPerformed(e);
616 invertSequenceMenuItem.setText("Invert Sequence Selection");
617 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
618 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
619 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
620 invertSequenceMenuItem
621 .addActionListener(new java.awt.event.ActionListener()
623 public void actionPerformed(ActionEvent e)
625 invertSequenceMenuItem_actionPerformed(e);
628 grpsFromSelection.setText("Make Groups for selection");
629 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
631 public void actionPerformed(ActionEvent e)
633 makeGrpsFromSelection_actionPerformed(e);
637 remove2LeftMenuItem.setText("Remove Left");
638 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
639 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
640 .getMenuShortcutKeyMask(), false));
642 .addActionListener(new java.awt.event.ActionListener()
644 public void actionPerformed(ActionEvent e)
646 remove2LeftMenuItem_actionPerformed(e);
649 remove2RightMenuItem.setText("Remove Right");
650 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
651 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
652 .getMenuShortcutKeyMask(), false));
654 .addActionListener(new java.awt.event.ActionListener()
656 public void actionPerformed(ActionEvent e)
658 remove2RightMenuItem_actionPerformed(e);
661 removeGappedColumnMenuItem.setText("Remove Empty Columns");
662 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
663 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
664 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
665 removeGappedColumnMenuItem
666 .addActionListener(new java.awt.event.ActionListener()
668 public void actionPerformed(ActionEvent e)
670 removeGappedColumnMenuItem_actionPerformed(e);
673 removeAllGapsMenuItem.setText("Remove All Gaps");
674 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
675 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
676 .getDefaultToolkit().getMenuShortcutKeyMask()
677 | java.awt.event.KeyEvent.SHIFT_MASK, false));
678 removeAllGapsMenuItem
679 .addActionListener(new java.awt.event.ActionListener()
681 public void actionPerformed(ActionEvent e)
683 removeAllGapsMenuItem_actionPerformed(e);
686 justifyLeftMenuItem.setText("Left Justify Alignment");
688 .addActionListener(new java.awt.event.ActionListener()
690 public void actionPerformed(ActionEvent e)
692 justifyLeftMenuItem_actionPerformed(e);
695 justifyRightMenuItem.setText("Right Justify Alignment");
697 .addActionListener(new java.awt.event.ActionListener()
699 public void actionPerformed(ActionEvent e)
701 justifyRightMenuItem_actionPerformed(e);
704 viewBoxesMenuItem.setText("Boxes");
705 viewBoxesMenuItem.setState(true);
706 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
708 public void actionPerformed(ActionEvent e)
710 viewBoxesMenuItem_actionPerformed(e);
713 viewTextMenuItem.setText("Text");
714 viewTextMenuItem.setState(true);
715 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
717 public void actionPerformed(ActionEvent e)
719 viewTextMenuItem_actionPerformed(e);
722 showNonconservedMenuItem.setText("Show nonconserved");
723 showNonconservedMenuItem.setState(false);
724 showNonconservedMenuItem
725 .addActionListener(new java.awt.event.ActionListener()
727 public void actionPerformed(ActionEvent e)
729 showUnconservedMenuItem_actionPerformed(e);
732 sortPairwiseMenuItem.setText("by Pairwise Identity");
734 .addActionListener(new java.awt.event.ActionListener()
736 public void actionPerformed(ActionEvent e)
738 sortPairwiseMenuItem_actionPerformed(e);
741 sortIDMenuItem.setText("by ID");
742 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
744 public void actionPerformed(ActionEvent e)
746 sortIDMenuItem_actionPerformed(e);
749 sortLengthMenuItem.setText("By Length");
751 .addActionListener(new java.awt.event.ActionListener()
753 public void actionPerformed(ActionEvent e)
755 sortLengthMenuItem_actionPerformed(e);
758 sortGroupMenuItem.setText("by Group");
759 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
761 public void actionPerformed(ActionEvent e)
763 sortGroupMenuItem_actionPerformed(e);
766 removeRedundancyMenuItem.setText("Remove Redundancy...");
767 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
768 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
769 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
770 removeRedundancyMenuItem
771 .addActionListener(new java.awt.event.ActionListener()
773 public void actionPerformed(ActionEvent e)
775 removeRedundancyMenuItem_actionPerformed(e);
778 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
779 pairwiseAlignmentMenuItem
780 .addActionListener(new java.awt.event.ActionListener()
782 public void actionPerformed(ActionEvent e)
784 pairwiseAlignmentMenuItem_actionPerformed(e);
787 PCAMenuItem.setText("Principal Component Analysis");
788 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
790 public void actionPerformed(ActionEvent e)
792 PCAMenuItem_actionPerformed(e);
795 averageDistanceTreeMenuItem
796 .setText("Average Distance Using % Identity");
797 averageDistanceTreeMenuItem
798 .addActionListener(new java.awt.event.ActionListener()
800 public void actionPerformed(ActionEvent e)
802 averageDistanceTreeMenuItem_actionPerformed(e);
805 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
806 neighbourTreeMenuItem
807 .addActionListener(new java.awt.event.ActionListener()
809 public void actionPerformed(ActionEvent e)
811 neighbourTreeMenuItem_actionPerformed(e);
814 this.getContentPane().setLayout(borderLayout1);
815 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
816 statusBar.setBackground(Color.white);
817 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
818 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
819 statusBar.setText("Status bar");
820 outputTextboxMenu.setText("Output to Textbox");
821 clustalColour.setText("Clustalx");
823 clustalColour.addActionListener(new java.awt.event.ActionListener()
825 public void actionPerformed(ActionEvent e)
827 clustalColour_actionPerformed(e);
830 zappoColour.setText("Zappo");
831 zappoColour.addActionListener(new java.awt.event.ActionListener()
833 public void actionPerformed(ActionEvent e)
835 zappoColour_actionPerformed(e);
838 taylorColour.setText("Taylor");
839 taylorColour.addActionListener(new java.awt.event.ActionListener()
841 public void actionPerformed(ActionEvent e)
843 taylorColour_actionPerformed(e);
846 hydrophobicityColour.setText("Hydrophobicity");
848 .addActionListener(new java.awt.event.ActionListener()
850 public void actionPerformed(ActionEvent e)
852 hydrophobicityColour_actionPerformed(e);
855 helixColour.setText("Helix Propensity");
856 helixColour.addActionListener(new java.awt.event.ActionListener()
858 public void actionPerformed(ActionEvent e)
860 helixColour_actionPerformed(e);
863 strandColour.setText("Strand Propensity");
864 strandColour.addActionListener(new java.awt.event.ActionListener()
866 public void actionPerformed(ActionEvent e)
868 strandColour_actionPerformed(e);
871 turnColour.setText("Turn Propensity");
872 turnColour.addActionListener(new java.awt.event.ActionListener()
874 public void actionPerformed(ActionEvent e)
876 turnColour_actionPerformed(e);
879 buriedColour.setText("Buried Index");
880 buriedColour.addActionListener(new java.awt.event.ActionListener()
882 public void actionPerformed(ActionEvent e)
884 buriedColour_actionPerformed(e);
887 userDefinedColour.setText("User Defined...");
888 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
890 public void actionPerformed(ActionEvent e)
892 userDefinedColour_actionPerformed(e);
895 PIDColour.setText("Percentage Identity");
896 PIDColour.addActionListener(new java.awt.event.ActionListener()
898 public void actionPerformed(ActionEvent e)
900 PIDColour_actionPerformed(e);
903 BLOSUM62Colour.setText("BLOSUM62 Score");
904 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
906 public void actionPerformed(ActionEvent e)
908 BLOSUM62Colour_actionPerformed(e);
911 nucleotideColour.setText("Nucleotide");
912 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
914 public void actionPerformed(ActionEvent e)
916 nucleotideColour_actionPerformed(e);
920 purinePyrimidineColour.setText("Purine/Pyrimidine");
921 purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
923 public void actionPerformed(ActionEvent e)
925 purinePyrimidineColour_actionPerformed(e);
929 RNAInteractionColour.setText("RNA Interaction type");
930 RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
932 public void actionPerformed(ActionEvent e)
934 RNAInteractionColour_actionPerformed(e);
938 * covariationColour.setText("Covariation");
939 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
940 * public void actionPerformed(ActionEvent e) {
941 * covariationColour_actionPerformed(e); } });
944 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
945 avDistanceTreeBlosumMenuItem
946 .addActionListener(new java.awt.event.ActionListener()
948 public void actionPerformed(ActionEvent e)
950 avTreeBlosumMenuItem_actionPerformed(e);
953 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
955 .addActionListener(new java.awt.event.ActionListener()
957 public void actionPerformed(ActionEvent e)
959 njTreeBlosumMenuItem_actionPerformed(e);
962 annotationPanelMenuItem.setActionCommand("");
963 annotationPanelMenuItem.setText("Show Annotations");
964 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
965 "SHOW_ANNOTATIONS", true));
966 annotationPanelMenuItem
967 .addActionListener(new java.awt.event.ActionListener()
969 public void actionPerformed(ActionEvent e)
971 annotationPanelMenuItem_actionPerformed(e);
974 colourTextMenuItem.setText("Colour Text");
976 .addActionListener(new java.awt.event.ActionListener()
978 public void actionPerformed(ActionEvent e)
980 colourTextMenuItem_actionPerformed(e);
983 htmlMenuItem.setText("HTML");
984 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
986 public void actionPerformed(ActionEvent e)
988 htmlMenuItem_actionPerformed(e);
991 overviewMenuItem.setText("Overview Window");
992 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
994 public void actionPerformed(ActionEvent e)
996 overviewMenuItem_actionPerformed(e);
999 undoMenuItem.setEnabled(false);
1000 undoMenuItem.setText("Undo");
1001 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1002 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1003 .getMenuShortcutKeyMask(), false));
1004 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1006 public void actionPerformed(ActionEvent e)
1008 undoMenuItem_actionPerformed(e);
1011 redoMenuItem.setEnabled(false);
1012 redoMenuItem.setText("Redo");
1013 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1014 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1015 .getMenuShortcutKeyMask(), false));
1016 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1018 public void actionPerformed(ActionEvent e)
1020 redoMenuItem_actionPerformed(e);
1023 conservationMenuItem.setText("By Conservation");
1024 conservationMenuItem
1025 .addActionListener(new java.awt.event.ActionListener()
1027 public void actionPerformed(ActionEvent e)
1029 conservationMenuItem_actionPerformed(e);
1032 noColourmenuItem.setText("None");
1033 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1035 public void actionPerformed(ActionEvent e)
1037 noColourmenuItem_actionPerformed(e);
1040 wrapMenuItem.setText("Wrap");
1041 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1043 public void actionPerformed(ActionEvent e)
1045 wrapMenuItem_actionPerformed(e);
1048 printMenuItem.setText("Print ...");
1049 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1050 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1051 .getMenuShortcutKeyMask(), false));
1052 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1054 public void actionPerformed(ActionEvent e)
1056 printMenuItem_actionPerformed(e);
1059 renderGapsMenuItem.setText("Show Gaps");
1060 renderGapsMenuItem.setState(true);
1062 .addActionListener(new java.awt.event.ActionListener()
1064 public void actionPerformed(ActionEvent e)
1066 renderGapsMenuItem_actionPerformed(e);
1069 findMenuItem.setText("Find...");
1070 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1071 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1072 .getMenuShortcutKeyMask(), false));
1073 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1075 public void actionPerformed(ActionEvent e)
1077 findMenuItem_actionPerformed(e);
1080 abovePIDThreshold.setText("Above Identity Threshold");
1081 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1083 public void actionPerformed(ActionEvent e)
1085 abovePIDThreshold_actionPerformed(e);
1088 showSeqFeatures.setText("Show Sequence Features");
1089 showSeqFeatures.addActionListener(new ActionListener()
1091 public void actionPerformed(ActionEvent actionEvent)
1093 showSeqFeatures_actionPerformed(actionEvent);
1097 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1098 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1099 * void actionPerformed(ActionEvent actionEvent) {
1100 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1102 showDbRefsMenuitem.setText("Show Database Refs");
1103 showDbRefsMenuitem.addActionListener(new ActionListener()
1106 public void actionPerformed(ActionEvent e)
1108 showDbRefs_actionPerformed(e);
1112 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1113 showNpFeatsMenuitem.addActionListener(new ActionListener()
1116 public void actionPerformed(ActionEvent e)
1118 showNpFeats_actionPerformed(e);
1122 showGroupConservation.setText("Group Conservation");
1123 showGroupConservation.addActionListener(new ActionListener()
1126 public void actionPerformed(ActionEvent e)
1128 showGroupConservation_actionPerformed(e);
1133 showGroupConsensus.setText("Group Consensus");
1134 showGroupConsensus.addActionListener(new ActionListener()
1137 public void actionPerformed(ActionEvent e)
1139 showGroupConsensus_actionPerformed(e);
1143 showConsensusHistogram.setText("Show Consensus Histogram");
1144 showConsensusHistogram.addActionListener(new ActionListener()
1147 public void actionPerformed(ActionEvent e)
1149 showConsensusHistogram_actionPerformed(e);
1153 showSequenceLogo.setText("Show Consensus Logo");
1154 showSequenceLogo.addActionListener(new ActionListener()
1157 public void actionPerformed(ActionEvent e)
1159 showSequenceLogo_actionPerformed(e);
1163 normaliseSequenceLogo.setText("Normalise Consensus Logo");
1164 normaliseSequenceLogo.addActionListener(new ActionListener()
1167 public void actionPerformed(ActionEvent e)
1169 normaliseSequenceLogo_actionPerformed(e);
1173 applyAutoAnnotationSettings.setText("Apply to all groups");
1174 applyAutoAnnotationSettings.setState(false);
1175 applyAutoAnnotationSettings.setVisible(true);
1176 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1179 public void actionPerformed(ActionEvent e)
1181 applyAutoAnnotationSettings_actionPerformed(e);
1186 nucleotideColour.setText("Nucleotide");
1187 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1189 public void actionPerformed(ActionEvent e)
1191 nucleotideColour_actionPerformed(e);
1195 tcoffeeColour.setText("T-Coffee scores");
1196 tcoffeeColour.setEnabled(false);
1197 tcoffeeColour.addActionListener( new ActionListener() {
1200 public void actionPerformed(ActionEvent e) {
1201 tcoffeeColorScheme_actionPerformed(e);
1206 deleteGroups.setText("Undefine groups");
1207 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1208 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1209 .getMenuShortcutKeyMask(), false));
1210 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1212 public void actionPerformed(ActionEvent e)
1214 deleteGroups_actionPerformed(e);
1217 copy.setText("Copy");
1218 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1219 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1220 .getMenuShortcutKeyMask(), false));
1222 copy.addActionListener(new java.awt.event.ActionListener()
1224 public void actionPerformed(ActionEvent e)
1226 copy_actionPerformed(e);
1230 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1231 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1232 .getMenuShortcutKeyMask(), false));
1233 cut.addActionListener(new java.awt.event.ActionListener()
1235 public void actionPerformed(ActionEvent e)
1237 cut_actionPerformed(e);
1240 delete.setText("Delete");
1241 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1242 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1243 delete.addActionListener(new java.awt.event.ActionListener()
1245 public void actionPerformed(ActionEvent e)
1247 delete_actionPerformed(e);
1250 pasteMenu.setText("Paste");
1251 pasteNew.setText("To New Alignment");
1252 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1253 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1254 .getMenuShortcutKeyMask()
1255 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1256 pasteNew.addActionListener(new java.awt.event.ActionListener()
1258 public void actionPerformed(ActionEvent e)
1260 pasteNew_actionPerformed(e);
1263 pasteThis.setText("Add To This Alignment");
1264 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1265 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1266 .getMenuShortcutKeyMask(), false));
1267 pasteThis.addActionListener(new java.awt.event.ActionListener()
1269 public void actionPerformed(ActionEvent e)
1271 pasteThis_actionPerformed(e);
1274 applyToAllGroups.setText("Apply Colour To All Groups");
1275 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1277 public void actionPerformed(ActionEvent e)
1279 applyToAllGroups_actionPerformed(e);
1282 createPNG.addActionListener(new java.awt.event.ActionListener()
1284 public void actionPerformed(ActionEvent e)
1289 createPNG.setActionCommand("Save As PNG Image");
1290 createPNG.setText("PNG");
1291 font.setText("Font...");
1292 font.addActionListener(new java.awt.event.ActionListener()
1294 public void actionPerformed(ActionEvent e)
1296 font_actionPerformed(e);
1300 seqLimits.setText("Show Sequence Limits");
1301 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1302 seqLimits.addActionListener(new java.awt.event.ActionListener()
1304 public void actionPerformed(ActionEvent e)
1306 seqLimit_actionPerformed(e);
1309 epsFile.setText("EPS");
1310 epsFile.addActionListener(new java.awt.event.ActionListener()
1312 public void actionPerformed(ActionEvent e)
1317 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1318 LoadtreeMenuItem.setText("Load Associated Tree");
1319 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1321 public void actionPerformed(ActionEvent e)
1323 LoadtreeMenuItem_actionPerformed(e);
1327 scaleAbove.setVisible(false);
1328 scaleAbove.setText("Scale Above");
1329 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1331 public void actionPerformed(ActionEvent e)
1333 scaleAbove_actionPerformed(e);
1336 scaleLeft.setVisible(false);
1337 scaleLeft.setSelected(true);
1338 scaleLeft.setText("Scale Left");
1339 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1341 public void actionPerformed(ActionEvent e)
1343 scaleLeft_actionPerformed(e);
1346 scaleRight.setVisible(false);
1347 scaleRight.setSelected(true);
1348 scaleRight.setText("Scale Right");
1349 scaleRight.addActionListener(new java.awt.event.ActionListener()
1351 public void actionPerformed(ActionEvent e)
1353 scaleRight_actionPerformed(e);
1356 centreColumnLabelsMenuItem.setVisible(true);
1357 centreColumnLabelsMenuItem.setState(false);
1358 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1359 centreColumnLabelsMenuItem
1360 .addActionListener(new java.awt.event.ActionListener()
1362 public void actionPerformed(ActionEvent e)
1364 centreColumnLabels_actionPerformed(e);
1367 followHighlightMenuItem.setVisible(true);
1368 followHighlightMenuItem.setState(true);
1369 followHighlightMenuItem.setText("Automatic Scrolling");
1370 followHighlightMenuItem.addActionListener(new ActionListener()
1373 public void actionPerformed(ActionEvent e)
1375 followHighlight_actionPerformed();
1380 modifyPID.setText("Modify Identity Threshold...");
1381 modifyPID.addActionListener(new java.awt.event.ActionListener()
1383 public void actionPerformed(ActionEvent e)
1385 modifyPID_actionPerformed(e);
1388 modifyConservation.setText("Modify Conservation Threshold...");
1390 .addActionListener(new java.awt.event.ActionListener()
1392 public void actionPerformed(ActionEvent e)
1394 modifyConservation_actionPerformed(e);
1397 sortByTreeMenu.setText("By Tree Order");
1398 sort.setText("Sort");
1399 sort.addMenuListener(new MenuListener()
1401 public void menuSelected(MenuEvent e)
1406 public void menuDeselected(MenuEvent e)
1410 public void menuCanceled(MenuEvent e)
1414 sortByAnnotScore.setText("by Score");
1415 sort.add(sortByAnnotScore);
1416 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1419 public void menuCanceled(MenuEvent e)
1423 public void menuDeselected(MenuEvent e)
1427 public void menuSelected(MenuEvent e)
1429 buildSortByAnnotationScoresMenu();
1432 sortByAnnotScore.setVisible(false);
1434 calculateTree.setText("Calculate Tree");
1436 jMenu2.setText("Export Image");
1437 padGapsMenuitem.setText("Pad Gaps");
1438 padGapsMenuitem.setState(jalview.bin.Cache
1439 .getDefault("PAD_GAPS", false));
1440 padGapsMenuitem.addActionListener(new ActionListener()
1442 public void actionPerformed(ActionEvent e)
1444 padGapsMenuitem_actionPerformed(e);
1447 vamsasStore.setVisible(false);
1448 vamsasStore.setText("VAMSAS store");
1449 vamsasStore.addActionListener(new ActionListener()
1451 public void actionPerformed(ActionEvent e)
1453 vamsasStore_actionPerformed(e);
1456 showTranslation.setText("Translate cDNA");
1457 showTranslation.addActionListener(new ActionListener()
1459 public void actionPerformed(ActionEvent e)
1461 showTranslation_actionPerformed(e);
1464 extractScores.setText("Extract Scores...");
1465 extractScores.addActionListener(new ActionListener()
1467 public void actionPerformed(ActionEvent e)
1469 extractScores_actionPerformed(e);
1472 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1474 showProducts.setText("Get Cross References");
1476 * showProducts.addActionListener(new ActionListener() {
1478 * public void actionPerformed(ActionEvent e) {
1479 * showProducts_actionPerformed(e); } });
1481 openFeatureSettings.setText("Feature Settings...");
1482 openFeatureSettings.addActionListener(new ActionListener()
1484 public void actionPerformed(ActionEvent e)
1486 featureSettings_actionPerformed(e);
1489 fetchSequence.setText("Fetch Sequence(s)...");
1490 fetchSequence.addActionListener(new ActionListener()
1492 public void actionPerformed(ActionEvent e)
1494 fetchSequence_actionPerformed(e);
1498 annotationColour.setText("By Annotation...");
1499 annotationColour.addActionListener(new ActionListener()
1501 public void actionPerformed(ActionEvent e)
1503 annotationColour_actionPerformed(e);
1507 rnahelicesColour.setText("By RNA helices");
1508 rnahelicesColour.addActionListener(new ActionListener()
1510 public void actionPerformed(ActionEvent e)
1512 rnahelicesColour_actionPerformed(e);
1516 associatedData.setText("Load Features / Annotations");
1517 associatedData.addActionListener(new ActionListener()
1519 public void actionPerformed(ActionEvent e)
1521 associatedData_actionPerformed(e);
1524 autoCalculate.setText("Autocalculate Consensus");
1525 autoCalculate.setState(jalview.bin.Cache.getDefault(
1526 "AUTO_CALC_CONSENSUS", true));
1527 autoCalculate.addActionListener(new ActionListener()
1529 public void actionPerformed(ActionEvent e)
1531 autoCalculate_actionPerformed(e);
1534 sortByTree.setText("Sort Alignment With New Tree");
1535 sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1536 sortByTree.setState(jalview.bin.Cache.getDefault(
1537 "SORT_BY_TREE", false));
1538 sortByTree.addActionListener(new ActionListener()
1540 public void actionPerformed(ActionEvent e)
1542 sortByTreeOption_actionPerformed(e);
1546 listenToViewSelections.setText("Listen for selections");
1547 listenToViewSelections.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1548 listenToViewSelections.setState(false);
1549 listenToViewSelections.addActionListener(new ActionListener()
1551 public void actionPerformed(ActionEvent e)
1553 listenToViewSelections_actionPerformed(e);
1557 addSequenceMenu.setText("Add Sequences");
1558 addFromFile.setText("From File");
1559 addFromFile.addActionListener(new ActionListener()
1561 public void actionPerformed(ActionEvent e)
1563 addFromFile_actionPerformed(e);
1566 addFromText.setText("From Textbox");
1567 addFromText.addActionListener(new ActionListener()
1569 public void actionPerformed(ActionEvent e)
1571 addFromText_actionPerformed(e);
1574 addFromURL.setText("From URL");
1575 addFromURL.addActionListener(new ActionListener()
1577 public void actionPerformed(ActionEvent e)
1579 addFromURL_actionPerformed(e);
1582 exportFeatures.setText("Export Features...");
1583 exportFeatures.addActionListener(new ActionListener()
1585 public void actionPerformed(ActionEvent e)
1587 exportFeatures_actionPerformed(e);
1590 exportAnnotations.setText("Export Annotations...");
1591 exportAnnotations.addActionListener(new ActionListener()
1593 public void actionPerformed(ActionEvent e)
1595 exportAnnotations_actionPerformed(e);
1598 statusPanel.setLayout(gridLayout1);
1599 jMenu3.setText("Show");
1600 showAllSeqs.setText("All Sequences");
1601 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1602 showAllSeqs.addActionListener(new ActionListener()
1604 public void actionPerformed(ActionEvent e)
1606 showAllSeqs_actionPerformed(e);
1609 showAllColumns.setText("All Columns");
1610 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1611 showAllColumns.addActionListener(new ActionListener()
1613 public void actionPerformed(ActionEvent e)
1615 showAllColumns_actionPerformed(e);
1618 hideMenu.setText("Hide");
1619 hideSelSequences.setText("Selected Sequences");
1620 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1621 hideSelSequences.addActionListener(new ActionListener()
1623 public void actionPerformed(ActionEvent e)
1625 hideSelSequences_actionPerformed(e);
1628 hideSelColumns.setText("Selected Columns");
1629 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1630 hideSelColumns.addActionListener(new ActionListener()
1632 public void actionPerformed(ActionEvent e)
1634 hideSelColumns_actionPerformed(e);
1637 hideAllSelection.setText("Selected Region");
1638 hideAllSelection.addActionListener(new ActionListener()
1640 public void actionPerformed(ActionEvent e)
1642 hideAllSelection_actionPerformed(e);
1645 // TODO: should be hidden if no selection exists.
1646 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1647 hideAllButSelection.addActionListener(new ActionListener()
1649 public void actionPerformed(ActionEvent e)
1651 hideAllButSelection_actionPerformed(e);
1654 showAllhidden.setText("All Sequences and Columns");
1656 .setToolTipText("H toggles visibility of hidden or selected regions.");
1657 showAllhidden.addActionListener(new ActionListener()
1659 public void actionPerformed(ActionEvent e)
1661 showAllhidden_actionPerformed(e);
1665 hiddenMarkers.setText("Show Hidden Markers");
1666 hiddenMarkers.addActionListener(new ActionListener()
1668 public void actionPerformed(ActionEvent e)
1670 hiddenMarkers_actionPerformed(e);
1673 invertColSel.setText("Invert Column Selection");
1674 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1675 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1676 .getMenuShortcutKeyMask()
1677 | java.awt.event.KeyEvent.ALT_MASK, false));
1678 invertColSel.addActionListener(new ActionListener()
1680 public void actionPerformed(ActionEvent e)
1682 invertColSel_actionPerformed(e);
1685 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1687 public void stateChanged(ChangeEvent evt)
1689 JTabbedPane pane = (JTabbedPane) evt.getSource();
1690 int sel = pane.getSelectedIndex();
1691 tabSelectionChanged(sel);
1694 tabbedPane.addMouseListener(new MouseAdapter()
1696 public void mousePressed(MouseEvent e)
1698 tabbedPane_mousePressed(e);
1701 tabbedPane.addFocusListener(new FocusAdapter()
1703 public void focusGained(FocusEvent e)
1705 tabbedPane_focusGained(e);
1708 save.setText("Save");
1709 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1710 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1711 .getMenuShortcutKeyMask(), false));
1712 save.addActionListener(new ActionListener()
1714 public void actionPerformed(ActionEvent e)
1716 save_actionPerformed(e);
1719 reload.setEnabled(false);
1720 reload.setText("Reload");
1721 reload.addActionListener(new ActionListener()
1723 public void actionPerformed(ActionEvent e)
1725 reload_actionPerformed(e);
1728 newView.setText("New View");
1729 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1730 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1731 .getMenuShortcutKeyMask(), false));
1732 newView.addActionListener(new ActionListener()
1734 public void actionPerformed(ActionEvent e)
1736 newView_actionPerformed(e);
1739 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1740 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1741 textColour.setText("Colour Text ...");
1742 textColour.addActionListener(new ActionListener()
1744 public void actionPerformed(ActionEvent e)
1746 textColour_actionPerformed(e);
1749 formatMenu.setText("Format");
1750 selectMenu.setText("Select");
1751 idRightAlign.setText("Right Align Sequence Id");
1752 idRightAlign.addActionListener(new ActionListener()
1754 public void actionPerformed(ActionEvent e)
1756 idRightAlign_actionPerformed(e);
1759 gatherViews.setEnabled(false);
1760 gatherViews.setText("Gather Views");
1761 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1762 java.awt.event.KeyEvent.VK_G, 0, false));
1763 gatherViews.addActionListener(new ActionListener()
1765 public void actionPerformed(ActionEvent e)
1767 gatherViews_actionPerformed(e);
1770 expandViews.setEnabled(false);
1771 expandViews.setText("Expand Views");
1772 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1773 java.awt.event.KeyEvent.VK_X, 0, false));
1774 expandViews.addActionListener(new ActionListener()
1776 public void actionPerformed(ActionEvent e)
1778 expandViews_actionPerformed(e);
1781 pageSetup.setText("Page Setup ...");
1782 pageSetup.addActionListener(new ActionListener()
1784 public void actionPerformed(ActionEvent e)
1786 pageSetup_actionPerformed(e);
1789 alignmentProperties.setText("Alignment Properties...");
1790 alignmentProperties.addActionListener(new ActionListener()
1792 public void actionPerformed(ActionEvent actionEvent)
1794 alignmentProperties();
1797 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1798 autoAnnMenu.setText("Autocalculated Annotation");
1799 alignFrameMenuBar.add(fileMenu);
1800 alignFrameMenuBar.add(editMenu);
1801 alignFrameMenuBar.add(selectMenu);
1802 alignFrameMenuBar.add(viewMenu);
1803 alignFrameMenuBar.add(formatMenu);
1804 alignFrameMenuBar.add(colourMenu);
1805 alignFrameMenuBar.add(calculateMenu);
1806 alignFrameMenuBar.add(webService);
1807 fileMenu.add(fetchSequence);
1808 fileMenu.add(addSequenceMenu);
1809 fileMenu.add(reload);
1810 fileMenu.addSeparator();
1811 fileMenu.add(vamsasStore);
1813 fileMenu.add(saveAs);
1814 fileMenu.add(outputTextboxMenu);
1815 fileMenu.add(pageSetup);
1816 fileMenu.add(printMenuItem);
1817 fileMenu.addSeparator();
1818 fileMenu.add(jMenu2);
1819 fileMenu.add(exportFeatures);
1820 fileMenu.add(exportAnnotations);
1821 fileMenu.add(LoadtreeMenuItem);
1822 fileMenu.add(associatedData);
1823 fileMenu.addSeparator();
1824 fileMenu.add(closeMenuItem);
1825 editMenu.add(undoMenuItem);
1826 editMenu.add(redoMenuItem);
1829 editMenu.add(pasteMenu);
1830 editMenu.add(delete);
1831 editMenu.addSeparator();
1832 editMenu.add(remove2LeftMenuItem);
1833 editMenu.add(remove2RightMenuItem);
1834 editMenu.add(removeGappedColumnMenuItem);
1835 editMenu.add(removeAllGapsMenuItem);
1836 editMenu.add(removeRedundancyMenuItem);
1837 editMenu.addSeparator();
1838 // dont add these yet in the CVS build - they cannot be undone!
1839 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1840 // editMenu.add(justifyLeftMenuItem);
1841 // editMenu.add(justifyRightMenuItem);
1842 // editMenu.addSeparator();
1843 editMenu.add(padGapsMenuitem);
1844 viewMenu.add(newView);
1845 viewMenu.add(expandViews);
1846 viewMenu.add(gatherViews);
1847 viewMenu.addSeparator();
1848 viewMenu.add(jMenu3);
1849 viewMenu.add(hideMenu);
1850 viewMenu.addSeparator();
1851 viewMenu.add(followHighlightMenuItem);
1852 viewMenu.add(annotationPanelMenuItem);
1853 autoAnnMenu.add(applyAutoAnnotationSettings);
1854 autoAnnMenu.add(showConsensusHistogram);
1855 autoAnnMenu.add(showSequenceLogo);
1856 autoAnnMenu.add(normaliseSequenceLogo);
1857 autoAnnMenu.addSeparator();
1858 autoAnnMenu.add(showGroupConservation);
1859 autoAnnMenu.add(showGroupConsensus);
1860 viewMenu.add(autoAnnMenu);
1861 viewMenu.addSeparator();
1862 viewMenu.add(showSeqFeatures);
1863 // viewMenu.add(showSeqFeaturesHeight);
1865 viewMenu.add(openFeatureSettings);
1866 tooltipSettingsMenu.add(showDbRefsMenuitem);
1867 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1868 viewMenu.add(tooltipSettingsMenu);
1869 viewMenu.addSeparator();
1870 viewMenu.add(alignmentProperties);
1871 viewMenu.addSeparator();
1872 viewMenu.add(overviewMenuItem);
1873 colourMenu.add(applyToAllGroups);
1874 colourMenu.add(textColour);
1875 colourMenu.addSeparator();
1876 colourMenu.add(noColourmenuItem);
1877 colourMenu.add(clustalColour);
1878 colourMenu.add(BLOSUM62Colour);
1879 colourMenu.add(PIDColour);
1880 colourMenu.add(zappoColour);
1881 colourMenu.add(taylorColour);
1882 colourMenu.add(hydrophobicityColour);
1883 colourMenu.add(helixColour);
1884 colourMenu.add(strandColour);
1885 colourMenu.add(turnColour);
1886 colourMenu.add(buriedColour);
1887 colourMenu.add(nucleotideColour);
1888 colourMenu.add(purinePyrimidineColour);
1889 colourMenu.add(RNAInteractionColour);
1890 // colourMenu.add(covariationColour);
1891 colourMenu.add(tcoffeeColour);
1892 colourMenu.add(userDefinedColour);
1893 colourMenu.addSeparator();
1894 colourMenu.add(conservationMenuItem);
1895 colourMenu.add(modifyConservation);
1896 colourMenu.add(abovePIDThreshold);
1897 colourMenu.add(modifyPID);
1898 colourMenu.add(annotationColour);
1899 colourMenu.add(rnahelicesColour);
1900 calculateMenu.add(sort);
1901 calculateMenu.add(calculateTree);
1902 calculateMenu.addSeparator();
1903 calculateMenu.add(pairwiseAlignmentMenuItem);
1904 calculateMenu.add(PCAMenuItem);
1905 calculateMenu.addSeparator();
1906 calculateMenu.add(showTranslation);
1907 calculateMenu.add(showProducts);
1908 calculateMenu.add(autoCalculate);
1909 calculateMenu.add(sortByTree);
1910 calculateMenu.addSeparator();
1911 calculateMenu.add(extractScores);
1912 webServiceNoServices = new JMenuItem("<No Services>");
1913 webService.add(webServiceNoServices);
1914 pasteMenu.add(pasteNew);
1915 pasteMenu.add(pasteThis);
1916 sort.add(sortIDMenuItem);
1917 sort.add(sortLengthMenuItem);
1918 sort.add(sortGroupMenuItem);
1919 sort.add(sortPairwiseMenuItem);
1920 sort.add(sortByTreeMenu);
1921 calculateTree.add(averageDistanceTreeMenuItem);
1922 calculateTree.add(neighbourTreeMenuItem);
1923 calculateTree.add(avDistanceTreeBlosumMenuItem);
1924 calculateTree.add(njTreeBlosumMenuItem);
1925 jMenu2.add(htmlMenuItem);
1926 jMenu2.add(epsFile);
1927 jMenu2.add(createPNG);
1928 addSequenceMenu.add(addFromFile);
1929 addSequenceMenu.add(addFromText);
1930 addSequenceMenu.add(addFromURL);
1931 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1932 statusPanel.add(statusBar, null);
1933 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1934 jMenu3.add(showAllColumns);
1935 jMenu3.add(showAllSeqs);
1936 jMenu3.add(showAllhidden);
1937 hideMenu.add(hideSelColumns);
1938 hideMenu.add(hideSelSequences);
1939 hideMenu.add(hideAllSelection);
1940 hideMenu.add(hideAllButSelection);
1942 formatMenu.add(font);
1943 formatMenu.addSeparator();
1944 formatMenu.add(wrapMenuItem);
1945 formatMenu.add(scaleAbove);
1946 formatMenu.add(scaleLeft);
1947 formatMenu.add(scaleRight);
1948 formatMenu.add(seqLimits);
1949 formatMenu.add(idRightAlign);
1950 formatMenu.add(hiddenMarkers);
1951 formatMenu.add(viewBoxesMenuItem);
1952 formatMenu.add(viewTextMenuItem);
1953 formatMenu.add(colourTextMenuItem);
1954 formatMenu.add(renderGapsMenuItem);
1955 formatMenu.add(centreColumnLabelsMenuItem);
1956 formatMenu.add(showNonconservedMenuItem);
1957 selectMenu.add(findMenuItem);
1958 selectMenu.addSeparator();
1959 selectMenu.add(selectAllSequenceMenuItem);
1960 selectMenu.add(deselectAllSequenceMenuItem);
1961 selectMenu.add(invertSequenceMenuItem);
1962 selectMenu.add(invertColSel);
1963 selectMenu.add(deleteGroups);
1964 selectMenu.add(grpsFromSelection);
1965 // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
1966 //selectMenu.addSeparator();
1967 //selectMenu.add(listenToViewSelections);
1970 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1972 // TODO Auto-generated method stub
1976 protected void listenToViewSelections_actionPerformed(ActionEvent e)
1978 // TODO Auto-generated method stub
1982 protected void showAllhidden_actionPerformed(ActionEvent e)
1984 // TODO Auto-generated method stub
1988 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1990 // TODO Auto-generated method stub
1994 protected void hideAllSelection_actionPerformed(ActionEvent e)
1996 // TODO Auto-generated method stub
2000 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2002 // TODO Auto-generated method stub
2006 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2008 // TODO Auto-generated method stub
2012 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2014 // TODO Auto-generated method stub
2018 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2020 // TODO Auto-generated method stub
2024 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2026 // TODO Auto-generated method stub
2030 protected void showGroupConservation_actionPerformed(ActionEvent e)
2032 // TODO Auto-generated method stub
2036 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2038 // TODO Auto-generated method stub
2042 protected void showSeqFeaturesHeight_actionPerformed(
2043 ActionEvent actionEvent)
2045 // TODO Auto-generated method stub
2049 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2051 // TODO Auto-generated method stub
2055 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2057 // TODO Auto-generated method stub
2061 protected void followHighlight_actionPerformed()
2063 // TODO Auto-generated method stub
2067 protected void showNpFeats_actionPerformed(ActionEvent e)
2069 // TODO Auto-generated method stub
2073 protected void showDbRefs_actionPerformed(ActionEvent e)
2075 // TODO Auto-generated method stub
2079 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2083 protected void showProducts_actionPerformed(ActionEvent e)
2087 protected void buildSortByAnnotationScoresMenu()
2091 protected void extractScores_actionPerformed(ActionEvent e)
2095 protected void outputText_actionPerformed(ActionEvent e)
2099 public void addFromFile_actionPerformed(ActionEvent e)
2104 public void addFromText_actionPerformed(ActionEvent e)
2109 public void addFromURL_actionPerformed(ActionEvent e)
2114 public void exportFeatures_actionPerformed(ActionEvent e)
2119 public void exportAnnotations_actionPerformed(ActionEvent e)
2124 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2128 protected void closeMenuItem_actionPerformed(boolean b)
2132 protected void redoMenuItem_actionPerformed(ActionEvent e)
2136 protected void undoMenuItem_actionPerformed(ActionEvent e)
2140 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2144 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2148 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2152 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2156 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2160 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2164 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2168 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2172 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2176 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2180 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2184 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2188 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2192 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2196 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2200 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2204 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2208 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2212 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2216 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2220 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2224 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2228 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2232 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2236 protected void clustalColour_actionPerformed(ActionEvent e)
2240 protected void zappoColour_actionPerformed(ActionEvent e)
2244 protected void taylorColour_actionPerformed(ActionEvent e)
2248 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2252 protected void helixColour_actionPerformed(ActionEvent e)
2256 protected void strandColour_actionPerformed(ActionEvent e)
2260 protected void turnColour_actionPerformed(ActionEvent e)
2264 protected void buriedColour_actionPerformed(ActionEvent e)
2268 protected void userDefinedColour_actionPerformed(ActionEvent e)
2272 protected void PIDColour_actionPerformed(ActionEvent e)
2276 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2280 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2284 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2290 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2293 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2297 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2301 protected void printMenuItem_actionPerformed(ActionEvent e)
2305 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2309 protected void findMenuItem_actionPerformed(ActionEvent e)
2313 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2317 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2321 protected void nucleotideColour_actionPerformed(ActionEvent e)
2325 protected void deleteGroups_actionPerformed(ActionEvent e)
2329 protected void copy_actionPerformed(ActionEvent e)
2333 protected void cut_actionPerformed(ActionEvent e)
2337 protected void delete_actionPerformed(ActionEvent e)
2341 protected void pasteNew_actionPerformed(ActionEvent e)
2345 protected void pasteThis_actionPerformed(ActionEvent e)
2349 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2353 public void createPNG(java.io.File f)
2357 protected void font_actionPerformed(ActionEvent e)
2361 protected void seqLimit_actionPerformed(ActionEvent e)
2365 public void seqDBRef_actionPerformed(ActionEvent e)
2370 public void createEPS(java.io.File f)
2374 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2380 * Template method to handle the 'load T-Coffee scores' menu event.
2382 * Subclasses override this method to provide a custom action.
2384 * @param event The raised event
2386 protected void loadScores_actionPerformed(ActionEvent event) {
2392 * Template method to handle the 'Color T-Coffee scores' menu event.
2394 * Subclasses override this method to provide a custom action.
2396 * @param event The raised event
2398 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) {
2403 protected void jpred_actionPerformed(ActionEvent e)
2407 protected void scaleAbove_actionPerformed(ActionEvent e)
2411 protected void scaleLeft_actionPerformed(ActionEvent e)
2415 protected void scaleRight_actionPerformed(ActionEvent e)
2419 protected void modifyPID_actionPerformed(ActionEvent e)
2423 protected void modifyConservation_actionPerformed(ActionEvent e)
2427 protected void saveAs_actionPerformed(ActionEvent e)
2431 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2435 public void vamsasStore_actionPerformed(ActionEvent e)
2440 public void vamsasLoad_actionPerformed(ActionEvent e)
2445 public void showTranslation_actionPerformed(ActionEvent e)
2450 public void featureSettings_actionPerformed(ActionEvent e)
2455 public void fetchSequence_actionPerformed(ActionEvent e)
2460 public void smoothFont_actionPerformed(ActionEvent e)
2465 public void annotationColour_actionPerformed(ActionEvent e)
2470 public void rnahelicesColour_actionPerformed(ActionEvent e)
2475 public void associatedData_actionPerformed(ActionEvent e)
2480 public void autoCalculate_actionPerformed(ActionEvent e)
2485 public void sortByTreeOption_actionPerformed(ActionEvent e)
2490 public void showAllSeqs_actionPerformed(ActionEvent e)
2495 public void showAllColumns_actionPerformed(ActionEvent e)
2500 public void hideSelSequences_actionPerformed(ActionEvent e)
2505 public void hideSelColumns_actionPerformed(ActionEvent e)
2510 public void hiddenMarkers_actionPerformed(ActionEvent e)
2515 public void findPdbId_actionPerformed(ActionEvent e)
2520 public void enterPdbId_actionPerformed(ActionEvent e)
2525 public void pdbFile_actionPerformed(ActionEvent e)
2530 public void invertColSel_actionPerformed(ActionEvent e)
2535 public void tabSelectionChanged(int sel)
2540 public void tabbedPane_mousePressed(MouseEvent e)
2545 public void tabbedPane_focusGained(FocusEvent e)
2550 public void save_actionPerformed(ActionEvent e)
2555 public void reload_actionPerformed(ActionEvent e)
2560 public void newView_actionPerformed(ActionEvent e)
2565 public void textColour_actionPerformed(ActionEvent e)
2570 public void idRightAlign_actionPerformed(ActionEvent e)
2575 public void expandViews_actionPerformed(ActionEvent e)
2580 public void gatherViews_actionPerformed(ActionEvent e)
2585 public void buildTreeMenu()
2590 public void pageSetup_actionPerformed(ActionEvent e)
2595 public void alignmentProperties()