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 alignFrameMenuBar.setBackground(Color.lightGray);
817 statusBar.setBackground(Color.white);
818 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
819 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
820 statusBar.setText("Status bar");
821 outputTextboxMenu.setText("Output to Textbox");
822 clustalColour.setText("Clustalx");
824 clustalColour.addActionListener(new java.awt.event.ActionListener()
826 public void actionPerformed(ActionEvent e)
828 clustalColour_actionPerformed(e);
831 zappoColour.setText("Zappo");
832 zappoColour.addActionListener(new java.awt.event.ActionListener()
834 public void actionPerformed(ActionEvent e)
836 zappoColour_actionPerformed(e);
839 taylorColour.setText("Taylor");
840 taylorColour.addActionListener(new java.awt.event.ActionListener()
842 public void actionPerformed(ActionEvent e)
844 taylorColour_actionPerformed(e);
847 hydrophobicityColour.setText("Hydrophobicity");
849 .addActionListener(new java.awt.event.ActionListener()
851 public void actionPerformed(ActionEvent e)
853 hydrophobicityColour_actionPerformed(e);
856 helixColour.setText("Helix Propensity");
857 helixColour.addActionListener(new java.awt.event.ActionListener()
859 public void actionPerformed(ActionEvent e)
861 helixColour_actionPerformed(e);
864 strandColour.setText("Strand Propensity");
865 strandColour.addActionListener(new java.awt.event.ActionListener()
867 public void actionPerformed(ActionEvent e)
869 strandColour_actionPerformed(e);
872 turnColour.setText("Turn Propensity");
873 turnColour.addActionListener(new java.awt.event.ActionListener()
875 public void actionPerformed(ActionEvent e)
877 turnColour_actionPerformed(e);
880 buriedColour.setText("Buried Index");
881 buriedColour.addActionListener(new java.awt.event.ActionListener()
883 public void actionPerformed(ActionEvent e)
885 buriedColour_actionPerformed(e);
888 userDefinedColour.setText("User Defined...");
889 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
891 public void actionPerformed(ActionEvent e)
893 userDefinedColour_actionPerformed(e);
896 PIDColour.setText("Percentage Identity");
897 PIDColour.addActionListener(new java.awt.event.ActionListener()
899 public void actionPerformed(ActionEvent e)
901 PIDColour_actionPerformed(e);
904 BLOSUM62Colour.setText("BLOSUM62 Score");
905 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
907 public void actionPerformed(ActionEvent e)
909 BLOSUM62Colour_actionPerformed(e);
912 nucleotideColour.setText("Nucleotide");
913 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
915 public void actionPerformed(ActionEvent e)
917 nucleotideColour_actionPerformed(e);
921 purinePyrimidineColour.setText("Purine/Pyrimidine");
922 purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
924 public void actionPerformed(ActionEvent e)
926 purinePyrimidineColour_actionPerformed(e);
930 RNAInteractionColour.setText("RNA Interaction type");
931 RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
933 public void actionPerformed(ActionEvent e)
935 RNAInteractionColour_actionPerformed(e);
939 * covariationColour.setText("Covariation");
940 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
941 * public void actionPerformed(ActionEvent e) {
942 * covariationColour_actionPerformed(e); } });
945 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
946 avDistanceTreeBlosumMenuItem
947 .addActionListener(new java.awt.event.ActionListener()
949 public void actionPerformed(ActionEvent e)
951 avTreeBlosumMenuItem_actionPerformed(e);
954 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
956 .addActionListener(new java.awt.event.ActionListener()
958 public void actionPerformed(ActionEvent e)
960 njTreeBlosumMenuItem_actionPerformed(e);
963 annotationPanelMenuItem.setActionCommand("");
964 annotationPanelMenuItem.setText("Show Annotations");
965 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
966 "SHOW_ANNOTATIONS", true));
967 annotationPanelMenuItem
968 .addActionListener(new java.awt.event.ActionListener()
970 public void actionPerformed(ActionEvent e)
972 annotationPanelMenuItem_actionPerformed(e);
975 colourTextMenuItem.setText("Colour Text");
977 .addActionListener(new java.awt.event.ActionListener()
979 public void actionPerformed(ActionEvent e)
981 colourTextMenuItem_actionPerformed(e);
984 htmlMenuItem.setText("HTML");
985 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
987 public void actionPerformed(ActionEvent e)
989 htmlMenuItem_actionPerformed(e);
992 overviewMenuItem.setText("Overview Window");
993 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
995 public void actionPerformed(ActionEvent e)
997 overviewMenuItem_actionPerformed(e);
1000 undoMenuItem.setEnabled(false);
1001 undoMenuItem.setText("Undo");
1002 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1003 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1004 .getMenuShortcutKeyMask(), false));
1005 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1007 public void actionPerformed(ActionEvent e)
1009 undoMenuItem_actionPerformed(e);
1012 redoMenuItem.setEnabled(false);
1013 redoMenuItem.setText("Redo");
1014 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1015 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1016 .getMenuShortcutKeyMask(), false));
1017 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1019 public void actionPerformed(ActionEvent e)
1021 redoMenuItem_actionPerformed(e);
1024 conservationMenuItem.setText("By Conservation");
1025 conservationMenuItem
1026 .addActionListener(new java.awt.event.ActionListener()
1028 public void actionPerformed(ActionEvent e)
1030 conservationMenuItem_actionPerformed(e);
1033 noColourmenuItem.setText("None");
1034 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1036 public void actionPerformed(ActionEvent e)
1038 noColourmenuItem_actionPerformed(e);
1041 wrapMenuItem.setText("Wrap");
1042 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1044 public void actionPerformed(ActionEvent e)
1046 wrapMenuItem_actionPerformed(e);
1049 printMenuItem.setText("Print ...");
1050 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1051 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1052 .getMenuShortcutKeyMask(), false));
1053 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1055 public void actionPerformed(ActionEvent e)
1057 printMenuItem_actionPerformed(e);
1060 renderGapsMenuItem.setText("Show Gaps");
1061 renderGapsMenuItem.setState(true);
1063 .addActionListener(new java.awt.event.ActionListener()
1065 public void actionPerformed(ActionEvent e)
1067 renderGapsMenuItem_actionPerformed(e);
1070 findMenuItem.setText("Find...");
1071 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1072 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1073 .getMenuShortcutKeyMask(), false));
1074 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1076 public void actionPerformed(ActionEvent e)
1078 findMenuItem_actionPerformed(e);
1081 abovePIDThreshold.setText("Above Identity Threshold");
1082 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1084 public void actionPerformed(ActionEvent e)
1086 abovePIDThreshold_actionPerformed(e);
1089 showSeqFeatures.setText("Show Sequence Features");
1090 showSeqFeatures.addActionListener(new ActionListener()
1092 public void actionPerformed(ActionEvent actionEvent)
1094 showSeqFeatures_actionPerformed(actionEvent);
1098 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1099 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1100 * void actionPerformed(ActionEvent actionEvent) {
1101 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1103 showDbRefsMenuitem.setText("Show Database Refs");
1104 showDbRefsMenuitem.addActionListener(new ActionListener()
1107 public void actionPerformed(ActionEvent e)
1109 showDbRefs_actionPerformed(e);
1113 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1114 showNpFeatsMenuitem.addActionListener(new ActionListener()
1117 public void actionPerformed(ActionEvent e)
1119 showNpFeats_actionPerformed(e);
1123 showGroupConservation.setText("Group Conservation");
1124 showGroupConservation.addActionListener(new ActionListener()
1127 public void actionPerformed(ActionEvent e)
1129 showGroupConservation_actionPerformed(e);
1134 showGroupConsensus.setText("Group Consensus");
1135 showGroupConsensus.addActionListener(new ActionListener()
1138 public void actionPerformed(ActionEvent e)
1140 showGroupConsensus_actionPerformed(e);
1144 showConsensusHistogram.setText("Show Consensus Histogram");
1145 showConsensusHistogram.addActionListener(new ActionListener()
1148 public void actionPerformed(ActionEvent e)
1150 showConsensusHistogram_actionPerformed(e);
1154 showSequenceLogo.setText("Show Consensus Logo");
1155 showSequenceLogo.addActionListener(new ActionListener()
1158 public void actionPerformed(ActionEvent e)
1160 showSequenceLogo_actionPerformed(e);
1164 normaliseSequenceLogo.setText("Normalise Consensus Logo");
1165 normaliseSequenceLogo.addActionListener(new ActionListener()
1168 public void actionPerformed(ActionEvent e)
1170 normaliseSequenceLogo_actionPerformed(e);
1174 applyAutoAnnotationSettings.setText("Apply to all groups");
1175 applyAutoAnnotationSettings.setState(false);
1176 applyAutoAnnotationSettings.setVisible(true);
1177 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1180 public void actionPerformed(ActionEvent e)
1182 applyAutoAnnotationSettings_actionPerformed(e);
1187 nucleotideColour.setText("Nucleotide");
1188 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1190 public void actionPerformed(ActionEvent e)
1192 nucleotideColour_actionPerformed(e);
1196 tcoffeeColour.setText("T-Coffee scores");
1197 tcoffeeColour.setEnabled(false);
1198 tcoffeeColour.addActionListener( new ActionListener() {
1201 public void actionPerformed(ActionEvent e) {
1202 tcoffeeColorScheme_actionPerformed(e);
1207 deleteGroups.setText("Undefine groups");
1208 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1209 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1210 .getMenuShortcutKeyMask(), false));
1211 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1213 public void actionPerformed(ActionEvent e)
1215 deleteGroups_actionPerformed(e);
1218 copy.setText("Copy");
1219 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1220 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1221 .getMenuShortcutKeyMask(), false));
1223 copy.addActionListener(new java.awt.event.ActionListener()
1225 public void actionPerformed(ActionEvent e)
1227 copy_actionPerformed(e);
1231 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1232 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1233 .getMenuShortcutKeyMask(), false));
1234 cut.addActionListener(new java.awt.event.ActionListener()
1236 public void actionPerformed(ActionEvent e)
1238 cut_actionPerformed(e);
1241 delete.setText("Delete");
1242 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1243 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1244 delete.addActionListener(new java.awt.event.ActionListener()
1246 public void actionPerformed(ActionEvent e)
1248 delete_actionPerformed(e);
1251 pasteMenu.setText("Paste");
1252 pasteNew.setText("To New Alignment");
1253 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1254 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1255 .getMenuShortcutKeyMask()
1256 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1257 pasteNew.addActionListener(new java.awt.event.ActionListener()
1259 public void actionPerformed(ActionEvent e)
1261 pasteNew_actionPerformed(e);
1264 pasteThis.setText("Add To This Alignment");
1265 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1266 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1267 .getMenuShortcutKeyMask(), false));
1268 pasteThis.addActionListener(new java.awt.event.ActionListener()
1270 public void actionPerformed(ActionEvent e)
1272 pasteThis_actionPerformed(e);
1275 applyToAllGroups.setText("Apply Colour To All Groups");
1276 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1278 public void actionPerformed(ActionEvent e)
1280 applyToAllGroups_actionPerformed(e);
1283 createPNG.addActionListener(new java.awt.event.ActionListener()
1285 public void actionPerformed(ActionEvent e)
1290 createPNG.setActionCommand("Save As PNG Image");
1291 createPNG.setText("PNG");
1292 font.setText("Font...");
1293 font.addActionListener(new java.awt.event.ActionListener()
1295 public void actionPerformed(ActionEvent e)
1297 font_actionPerformed(e);
1301 seqLimits.setText("Show Sequence Limits");
1302 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1303 seqLimits.addActionListener(new java.awt.event.ActionListener()
1305 public void actionPerformed(ActionEvent e)
1307 seqLimit_actionPerformed(e);
1310 epsFile.setText("EPS");
1311 epsFile.addActionListener(new java.awt.event.ActionListener()
1313 public void actionPerformed(ActionEvent e)
1318 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1319 LoadtreeMenuItem.setText("Load Associated Tree");
1320 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1322 public void actionPerformed(ActionEvent e)
1324 LoadtreeMenuItem_actionPerformed(e);
1328 scaleAbove.setVisible(false);
1329 scaleAbove.setText("Scale Above");
1330 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1332 public void actionPerformed(ActionEvent e)
1334 scaleAbove_actionPerformed(e);
1337 scaleLeft.setVisible(false);
1338 scaleLeft.setSelected(true);
1339 scaleLeft.setText("Scale Left");
1340 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1342 public void actionPerformed(ActionEvent e)
1344 scaleLeft_actionPerformed(e);
1347 scaleRight.setVisible(false);
1348 scaleRight.setSelected(true);
1349 scaleRight.setText("Scale Right");
1350 scaleRight.addActionListener(new java.awt.event.ActionListener()
1352 public void actionPerformed(ActionEvent e)
1354 scaleRight_actionPerformed(e);
1357 centreColumnLabelsMenuItem.setVisible(true);
1358 centreColumnLabelsMenuItem.setState(false);
1359 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1360 centreColumnLabelsMenuItem
1361 .addActionListener(new java.awt.event.ActionListener()
1363 public void actionPerformed(ActionEvent e)
1365 centreColumnLabels_actionPerformed(e);
1368 followHighlightMenuItem.setVisible(true);
1369 followHighlightMenuItem.setState(true);
1370 followHighlightMenuItem.setText("Automatic Scrolling");
1371 followHighlightMenuItem.addActionListener(new ActionListener()
1374 public void actionPerformed(ActionEvent e)
1376 followHighlight_actionPerformed();
1381 modifyPID.setText("Modify Identity Threshold...");
1382 modifyPID.addActionListener(new java.awt.event.ActionListener()
1384 public void actionPerformed(ActionEvent e)
1386 modifyPID_actionPerformed(e);
1389 modifyConservation.setText("Modify Conservation Threshold...");
1391 .addActionListener(new java.awt.event.ActionListener()
1393 public void actionPerformed(ActionEvent e)
1395 modifyConservation_actionPerformed(e);
1398 sortByTreeMenu.setText("By Tree Order");
1399 sort.setText("Sort");
1400 sort.addMenuListener(new MenuListener()
1402 public void menuSelected(MenuEvent e)
1407 public void menuDeselected(MenuEvent e)
1411 public void menuCanceled(MenuEvent e)
1415 sortByAnnotScore.setText("by Score");
1416 sort.add(sortByAnnotScore);
1417 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1420 public void menuCanceled(MenuEvent e)
1424 public void menuDeselected(MenuEvent e)
1428 public void menuSelected(MenuEvent e)
1430 buildSortByAnnotationScoresMenu();
1433 sortByAnnotScore.setVisible(false);
1435 calculateTree.setText("Calculate Tree");
1437 jMenu2.setText("Export Image");
1438 padGapsMenuitem.setText("Pad Gaps");
1439 padGapsMenuitem.setState(jalview.bin.Cache
1440 .getDefault("PAD_GAPS", false));
1441 padGapsMenuitem.addActionListener(new ActionListener()
1443 public void actionPerformed(ActionEvent e)
1445 padGapsMenuitem_actionPerformed(e);
1448 vamsasStore.setVisible(false);
1449 vamsasStore.setText("VAMSAS store");
1450 vamsasStore.addActionListener(new ActionListener()
1452 public void actionPerformed(ActionEvent e)
1454 vamsasStore_actionPerformed(e);
1457 showTranslation.setText("Translate cDNA");
1458 showTranslation.addActionListener(new ActionListener()
1460 public void actionPerformed(ActionEvent e)
1462 showTranslation_actionPerformed(e);
1465 extractScores.setText("Extract Scores...");
1466 extractScores.addActionListener(new ActionListener()
1468 public void actionPerformed(ActionEvent e)
1470 extractScores_actionPerformed(e);
1473 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1475 showProducts.setText("Get Cross References");
1477 * showProducts.addActionListener(new ActionListener() {
1479 * public void actionPerformed(ActionEvent e) {
1480 * showProducts_actionPerformed(e); } });
1482 openFeatureSettings.setText("Feature Settings...");
1483 openFeatureSettings.addActionListener(new ActionListener()
1485 public void actionPerformed(ActionEvent e)
1487 featureSettings_actionPerformed(e);
1490 fetchSequence.setText("Fetch Sequence(s)...");
1491 fetchSequence.addActionListener(new ActionListener()
1493 public void actionPerformed(ActionEvent e)
1495 fetchSequence_actionPerformed(e);
1499 annotationColour.setText("By Annotation...");
1500 annotationColour.addActionListener(new ActionListener()
1502 public void actionPerformed(ActionEvent e)
1504 annotationColour_actionPerformed(e);
1508 rnahelicesColour.setText("By RNA helices");
1509 rnahelicesColour.addActionListener(new ActionListener()
1511 public void actionPerformed(ActionEvent e)
1513 rnahelicesColour_actionPerformed(e);
1517 associatedData.setText("Load Features / Annotations");
1518 associatedData.addActionListener(new ActionListener()
1520 public void actionPerformed(ActionEvent e)
1522 associatedData_actionPerformed(e);
1525 autoCalculate.setText("Autocalculate Consensus");
1526 autoCalculate.setState(jalview.bin.Cache.getDefault(
1527 "AUTO_CALC_CONSENSUS", true));
1528 autoCalculate.addActionListener(new ActionListener()
1530 public void actionPerformed(ActionEvent e)
1532 autoCalculate_actionPerformed(e);
1535 sortByTree.setText("Sort Alignment With New Tree");
1536 sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1537 sortByTree.setState(jalview.bin.Cache.getDefault(
1538 "SORT_BY_TREE", false));
1539 sortByTree.addActionListener(new ActionListener()
1541 public void actionPerformed(ActionEvent e)
1543 sortByTreeOption_actionPerformed(e);
1547 listenToViewSelections.setText("Listen for selections");
1548 listenToViewSelections.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1549 listenToViewSelections.setState(false);
1550 listenToViewSelections.addActionListener(new ActionListener()
1552 public void actionPerformed(ActionEvent e)
1554 listenToViewSelections_actionPerformed(e);
1558 addSequenceMenu.setText("Add Sequences");
1559 addFromFile.setText("From File");
1560 addFromFile.addActionListener(new ActionListener()
1562 public void actionPerformed(ActionEvent e)
1564 addFromFile_actionPerformed(e);
1567 addFromText.setText("From Textbox");
1568 addFromText.addActionListener(new ActionListener()
1570 public void actionPerformed(ActionEvent e)
1572 addFromText_actionPerformed(e);
1575 addFromURL.setText("From URL");
1576 addFromURL.addActionListener(new ActionListener()
1578 public void actionPerformed(ActionEvent e)
1580 addFromURL_actionPerformed(e);
1583 exportFeatures.setText("Export Features...");
1584 exportFeatures.addActionListener(new ActionListener()
1586 public void actionPerformed(ActionEvent e)
1588 exportFeatures_actionPerformed(e);
1591 exportAnnotations.setText("Export Annotations...");
1592 exportAnnotations.addActionListener(new ActionListener()
1594 public void actionPerformed(ActionEvent e)
1596 exportAnnotations_actionPerformed(e);
1599 statusPanel.setLayout(gridLayout1);
1600 jMenu3.setText("Show");
1601 showAllSeqs.setText("All Sequences");
1602 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1603 showAllSeqs.addActionListener(new ActionListener()
1605 public void actionPerformed(ActionEvent e)
1607 showAllSeqs_actionPerformed(e);
1610 showAllColumns.setText("All Columns");
1611 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1612 showAllColumns.addActionListener(new ActionListener()
1614 public void actionPerformed(ActionEvent e)
1616 showAllColumns_actionPerformed(e);
1619 hideMenu.setText("Hide");
1620 hideSelSequences.setText("Selected Sequences");
1621 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1622 hideSelSequences.addActionListener(new ActionListener()
1624 public void actionPerformed(ActionEvent e)
1626 hideSelSequences_actionPerformed(e);
1629 hideSelColumns.setText("Selected Columns");
1630 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1631 hideSelColumns.addActionListener(new ActionListener()
1633 public void actionPerformed(ActionEvent e)
1635 hideSelColumns_actionPerformed(e);
1638 hideAllSelection.setText("Selected Region");
1639 hideAllSelection.addActionListener(new ActionListener()
1641 public void actionPerformed(ActionEvent e)
1643 hideAllSelection_actionPerformed(e);
1646 // TODO: should be hidden if no selection exists.
1647 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1648 hideAllButSelection.addActionListener(new ActionListener()
1650 public void actionPerformed(ActionEvent e)
1652 hideAllButSelection_actionPerformed(e);
1655 showAllhidden.setText("All Sequences and Columns");
1657 .setToolTipText("H toggles visibility of hidden or selected regions.");
1658 showAllhidden.addActionListener(new ActionListener()
1660 public void actionPerformed(ActionEvent e)
1662 showAllhidden_actionPerformed(e);
1666 hiddenMarkers.setText("Show Hidden Markers");
1667 hiddenMarkers.addActionListener(new ActionListener()
1669 public void actionPerformed(ActionEvent e)
1671 hiddenMarkers_actionPerformed(e);
1674 invertColSel.setText("Invert Column Selection");
1675 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1676 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1677 .getMenuShortcutKeyMask()
1678 | java.awt.event.KeyEvent.ALT_MASK, false));
1679 invertColSel.addActionListener(new ActionListener()
1681 public void actionPerformed(ActionEvent e)
1683 invertColSel_actionPerformed(e);
1686 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1688 public void stateChanged(ChangeEvent evt)
1690 JTabbedPane pane = (JTabbedPane) evt.getSource();
1691 int sel = pane.getSelectedIndex();
1692 tabSelectionChanged(sel);
1695 tabbedPane.addMouseListener(new MouseAdapter()
1697 public void mousePressed(MouseEvent e)
1699 tabbedPane_mousePressed(e);
1702 tabbedPane.addFocusListener(new FocusAdapter()
1704 public void focusGained(FocusEvent e)
1706 tabbedPane_focusGained(e);
1709 save.setText("Save");
1710 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1711 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1712 .getMenuShortcutKeyMask(), false));
1713 save.addActionListener(new ActionListener()
1715 public void actionPerformed(ActionEvent e)
1717 save_actionPerformed(e);
1720 reload.setEnabled(false);
1721 reload.setText("Reload");
1722 reload.addActionListener(new ActionListener()
1724 public void actionPerformed(ActionEvent e)
1726 reload_actionPerformed(e);
1729 newView.setText("New View");
1730 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1731 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1732 .getMenuShortcutKeyMask(), false));
1733 newView.addActionListener(new ActionListener()
1735 public void actionPerformed(ActionEvent e)
1737 newView_actionPerformed(e);
1740 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1741 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1742 textColour.setText("Colour Text ...");
1743 textColour.addActionListener(new ActionListener()
1745 public void actionPerformed(ActionEvent e)
1747 textColour_actionPerformed(e);
1750 formatMenu.setText("Format");
1751 selectMenu.setText("Select");
1752 idRightAlign.setText("Right Align Sequence Id");
1753 idRightAlign.addActionListener(new ActionListener()
1755 public void actionPerformed(ActionEvent e)
1757 idRightAlign_actionPerformed(e);
1760 gatherViews.setEnabled(false);
1761 gatherViews.setText("Gather Views");
1762 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1763 java.awt.event.KeyEvent.VK_G, 0, false));
1764 gatherViews.addActionListener(new ActionListener()
1766 public void actionPerformed(ActionEvent e)
1768 gatherViews_actionPerformed(e);
1771 expandViews.setEnabled(false);
1772 expandViews.setText("Expand Views");
1773 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1774 java.awt.event.KeyEvent.VK_X, 0, false));
1775 expandViews.addActionListener(new ActionListener()
1777 public void actionPerformed(ActionEvent e)
1779 expandViews_actionPerformed(e);
1782 pageSetup.setText("Page Setup ...");
1783 pageSetup.addActionListener(new ActionListener()
1785 public void actionPerformed(ActionEvent e)
1787 pageSetup_actionPerformed(e);
1790 alignmentProperties.setText("Alignment Properties...");
1791 alignmentProperties.addActionListener(new ActionListener()
1793 public void actionPerformed(ActionEvent actionEvent)
1795 alignmentProperties();
1798 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1799 autoAnnMenu.setText("Autocalculated Annotation");
1800 alignFrameMenuBar.add(fileMenu);
1801 alignFrameMenuBar.add(editMenu);
1802 alignFrameMenuBar.add(selectMenu);
1803 alignFrameMenuBar.add(viewMenu);
1804 alignFrameMenuBar.add(formatMenu);
1805 alignFrameMenuBar.add(colourMenu);
1806 alignFrameMenuBar.add(calculateMenu);
1807 alignFrameMenuBar.add(webService);
1808 fileMenu.add(fetchSequence);
1809 fileMenu.add(addSequenceMenu);
1810 fileMenu.add(reload);
1811 fileMenu.addSeparator();
1812 fileMenu.add(vamsasStore);
1814 fileMenu.add(saveAs);
1815 fileMenu.add(outputTextboxMenu);
1816 fileMenu.add(pageSetup);
1817 fileMenu.add(printMenuItem);
1818 fileMenu.addSeparator();
1819 fileMenu.add(jMenu2);
1820 fileMenu.add(exportFeatures);
1821 fileMenu.add(exportAnnotations);
1822 fileMenu.add(LoadtreeMenuItem);
1823 fileMenu.add(associatedData);
1824 fileMenu.addSeparator();
1825 fileMenu.add(closeMenuItem);
1826 editMenu.add(undoMenuItem);
1827 editMenu.add(redoMenuItem);
1830 editMenu.add(pasteMenu);
1831 editMenu.add(delete);
1832 editMenu.addSeparator();
1833 editMenu.add(remove2LeftMenuItem);
1834 editMenu.add(remove2RightMenuItem);
1835 editMenu.add(removeGappedColumnMenuItem);
1836 editMenu.add(removeAllGapsMenuItem);
1837 editMenu.add(removeRedundancyMenuItem);
1838 editMenu.addSeparator();
1839 // dont add these yet in the CVS build - they cannot be undone!
1840 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1841 // editMenu.add(justifyLeftMenuItem);
1842 // editMenu.add(justifyRightMenuItem);
1843 // editMenu.addSeparator();
1844 editMenu.add(padGapsMenuitem);
1845 viewMenu.add(newView);
1846 viewMenu.add(expandViews);
1847 viewMenu.add(gatherViews);
1848 viewMenu.addSeparator();
1849 viewMenu.add(jMenu3);
1850 viewMenu.add(hideMenu);
1851 viewMenu.addSeparator();
1852 viewMenu.add(followHighlightMenuItem);
1853 viewMenu.add(annotationPanelMenuItem);
1854 autoAnnMenu.add(applyAutoAnnotationSettings);
1855 autoAnnMenu.add(showConsensusHistogram);
1856 autoAnnMenu.add(showSequenceLogo);
1857 autoAnnMenu.add(normaliseSequenceLogo);
1858 autoAnnMenu.addSeparator();
1859 autoAnnMenu.add(showGroupConservation);
1860 autoAnnMenu.add(showGroupConsensus);
1861 viewMenu.add(autoAnnMenu);
1862 viewMenu.addSeparator();
1863 viewMenu.add(showSeqFeatures);
1864 // viewMenu.add(showSeqFeaturesHeight);
1866 viewMenu.add(openFeatureSettings);
1867 tooltipSettingsMenu.add(showDbRefsMenuitem);
1868 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1869 viewMenu.add(tooltipSettingsMenu);
1870 viewMenu.addSeparator();
1871 viewMenu.add(alignmentProperties);
1872 viewMenu.addSeparator();
1873 viewMenu.add(overviewMenuItem);
1874 colourMenu.add(applyToAllGroups);
1875 colourMenu.add(textColour);
1876 colourMenu.addSeparator();
1877 colourMenu.add(noColourmenuItem);
1878 colourMenu.add(clustalColour);
1879 colourMenu.add(BLOSUM62Colour);
1880 colourMenu.add(PIDColour);
1881 colourMenu.add(zappoColour);
1882 colourMenu.add(taylorColour);
1883 colourMenu.add(hydrophobicityColour);
1884 colourMenu.add(helixColour);
1885 colourMenu.add(strandColour);
1886 colourMenu.add(turnColour);
1887 colourMenu.add(buriedColour);
1888 colourMenu.add(nucleotideColour);
1889 colourMenu.add(purinePyrimidineColour);
1890 colourMenu.add(RNAInteractionColour);
1891 // colourMenu.add(covariationColour);
1892 colourMenu.add(tcoffeeColour);
1893 colourMenu.add(userDefinedColour);
1894 colourMenu.addSeparator();
1895 colourMenu.add(conservationMenuItem);
1896 colourMenu.add(modifyConservation);
1897 colourMenu.add(abovePIDThreshold);
1898 colourMenu.add(modifyPID);
1899 colourMenu.add(annotationColour);
1900 colourMenu.add(rnahelicesColour);
1901 calculateMenu.add(sort);
1902 calculateMenu.add(calculateTree);
1903 calculateMenu.addSeparator();
1904 calculateMenu.add(pairwiseAlignmentMenuItem);
1905 calculateMenu.add(PCAMenuItem);
1906 calculateMenu.addSeparator();
1907 calculateMenu.add(showTranslation);
1908 calculateMenu.add(showProducts);
1909 calculateMenu.add(autoCalculate);
1910 calculateMenu.add(sortByTree);
1911 calculateMenu.addSeparator();
1912 calculateMenu.add(extractScores);
1913 webServiceNoServices = new JMenuItem("<No Services>");
1914 webService.add(webServiceNoServices);
1915 pasteMenu.add(pasteNew);
1916 pasteMenu.add(pasteThis);
1917 sort.add(sortIDMenuItem);
1918 sort.add(sortLengthMenuItem);
1919 sort.add(sortGroupMenuItem);
1920 sort.add(sortPairwiseMenuItem);
1921 sort.add(sortByTreeMenu);
1922 calculateTree.add(averageDistanceTreeMenuItem);
1923 calculateTree.add(neighbourTreeMenuItem);
1924 calculateTree.add(avDistanceTreeBlosumMenuItem);
1925 calculateTree.add(njTreeBlosumMenuItem);
1926 jMenu2.add(htmlMenuItem);
1927 jMenu2.add(epsFile);
1928 jMenu2.add(createPNG);
1929 addSequenceMenu.add(addFromFile);
1930 addSequenceMenu.add(addFromText);
1931 addSequenceMenu.add(addFromURL);
1932 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1933 statusPanel.add(statusBar, null);
1934 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1935 jMenu3.add(showAllColumns);
1936 jMenu3.add(showAllSeqs);
1937 jMenu3.add(showAllhidden);
1938 hideMenu.add(hideSelColumns);
1939 hideMenu.add(hideSelSequences);
1940 hideMenu.add(hideAllSelection);
1941 hideMenu.add(hideAllButSelection);
1943 formatMenu.add(font);
1944 formatMenu.addSeparator();
1945 formatMenu.add(wrapMenuItem);
1946 formatMenu.add(scaleAbove);
1947 formatMenu.add(scaleLeft);
1948 formatMenu.add(scaleRight);
1949 formatMenu.add(seqLimits);
1950 formatMenu.add(idRightAlign);
1951 formatMenu.add(hiddenMarkers);
1952 formatMenu.add(viewBoxesMenuItem);
1953 formatMenu.add(viewTextMenuItem);
1954 formatMenu.add(colourTextMenuItem);
1955 formatMenu.add(renderGapsMenuItem);
1956 formatMenu.add(centreColumnLabelsMenuItem);
1957 formatMenu.add(showNonconservedMenuItem);
1958 selectMenu.add(findMenuItem);
1959 selectMenu.addSeparator();
1960 selectMenu.add(selectAllSequenceMenuItem);
1961 selectMenu.add(deselectAllSequenceMenuItem);
1962 selectMenu.add(invertSequenceMenuItem);
1963 selectMenu.add(invertColSel);
1964 selectMenu.add(deleteGroups);
1965 selectMenu.add(grpsFromSelection);
1966 // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
1967 //selectMenu.addSeparator();
1968 //selectMenu.add(listenToViewSelections);
1971 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1973 // TODO Auto-generated method stub
1977 protected void listenToViewSelections_actionPerformed(ActionEvent e)
1979 // TODO Auto-generated method stub
1983 protected void showAllhidden_actionPerformed(ActionEvent e)
1985 // TODO Auto-generated method stub
1989 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1991 // TODO Auto-generated method stub
1995 protected void hideAllSelection_actionPerformed(ActionEvent e)
1997 // TODO Auto-generated method stub
2001 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2003 // TODO Auto-generated method stub
2007 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2009 // TODO Auto-generated method stub
2013 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2015 // TODO Auto-generated method stub
2019 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2021 // TODO Auto-generated method stub
2025 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2027 // TODO Auto-generated method stub
2031 protected void showGroupConservation_actionPerformed(ActionEvent e)
2033 // TODO Auto-generated method stub
2037 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2039 // TODO Auto-generated method stub
2043 protected void showSeqFeaturesHeight_actionPerformed(
2044 ActionEvent actionEvent)
2046 // TODO Auto-generated method stub
2050 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2052 // TODO Auto-generated method stub
2056 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2058 // TODO Auto-generated method stub
2062 protected void followHighlight_actionPerformed()
2064 // TODO Auto-generated method stub
2068 protected void showNpFeats_actionPerformed(ActionEvent e)
2070 // TODO Auto-generated method stub
2074 protected void showDbRefs_actionPerformed(ActionEvent e)
2076 // TODO Auto-generated method stub
2080 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2084 protected void showProducts_actionPerformed(ActionEvent e)
2088 protected void buildSortByAnnotationScoresMenu()
2092 protected void extractScores_actionPerformed(ActionEvent e)
2096 protected void outputText_actionPerformed(ActionEvent e)
2100 public void addFromFile_actionPerformed(ActionEvent e)
2105 public void addFromText_actionPerformed(ActionEvent e)
2110 public void addFromURL_actionPerformed(ActionEvent e)
2115 public void exportFeatures_actionPerformed(ActionEvent e)
2120 public void exportAnnotations_actionPerformed(ActionEvent e)
2125 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2129 protected void closeMenuItem_actionPerformed(boolean b)
2133 protected void redoMenuItem_actionPerformed(ActionEvent e)
2137 protected void undoMenuItem_actionPerformed(ActionEvent e)
2141 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2145 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2149 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2153 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2157 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2161 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2165 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2169 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2173 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2177 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2181 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2185 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2189 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2193 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2197 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2201 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2205 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2209 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2213 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2217 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2221 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2225 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2229 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2233 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2237 protected void clustalColour_actionPerformed(ActionEvent e)
2241 protected void zappoColour_actionPerformed(ActionEvent e)
2245 protected void taylorColour_actionPerformed(ActionEvent e)
2249 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2253 protected void helixColour_actionPerformed(ActionEvent e)
2257 protected void strandColour_actionPerformed(ActionEvent e)
2261 protected void turnColour_actionPerformed(ActionEvent e)
2265 protected void buriedColour_actionPerformed(ActionEvent e)
2269 protected void userDefinedColour_actionPerformed(ActionEvent e)
2273 protected void PIDColour_actionPerformed(ActionEvent e)
2277 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2281 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2285 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2291 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2294 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2298 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2302 protected void printMenuItem_actionPerformed(ActionEvent e)
2306 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2310 protected void findMenuItem_actionPerformed(ActionEvent e)
2314 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2318 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2322 protected void nucleotideColour_actionPerformed(ActionEvent e)
2326 protected void deleteGroups_actionPerformed(ActionEvent e)
2330 protected void copy_actionPerformed(ActionEvent e)
2334 protected void cut_actionPerformed(ActionEvent e)
2338 protected void delete_actionPerformed(ActionEvent e)
2342 protected void pasteNew_actionPerformed(ActionEvent e)
2346 protected void pasteThis_actionPerformed(ActionEvent e)
2350 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2354 public void createPNG(java.io.File f)
2358 protected void font_actionPerformed(ActionEvent e)
2362 protected void seqLimit_actionPerformed(ActionEvent e)
2366 public void seqDBRef_actionPerformed(ActionEvent e)
2371 public void createEPS(java.io.File f)
2375 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2381 * Template method to handle the 'load T-Coffee scores' menu event.
2383 * Subclasses override this method to provide a custom action.
2385 * @param event The raised event
2387 protected void loadScores_actionPerformed(ActionEvent event) {
2393 * Template method to handle the 'Color T-Coffee scores' menu event.
2395 * Subclasses override this method to provide a custom action.
2397 * @param event The raised event
2399 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) {
2404 protected void jpred_actionPerformed(ActionEvent e)
2408 protected void scaleAbove_actionPerformed(ActionEvent e)
2412 protected void scaleLeft_actionPerformed(ActionEvent e)
2416 protected void scaleRight_actionPerformed(ActionEvent e)
2420 protected void modifyPID_actionPerformed(ActionEvent e)
2424 protected void modifyConservation_actionPerformed(ActionEvent e)
2428 protected void saveAs_actionPerformed(ActionEvent e)
2432 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2436 public void vamsasStore_actionPerformed(ActionEvent e)
2441 public void vamsasLoad_actionPerformed(ActionEvent e)
2446 public void showTranslation_actionPerformed(ActionEvent e)
2451 public void featureSettings_actionPerformed(ActionEvent e)
2456 public void fetchSequence_actionPerformed(ActionEvent e)
2461 public void smoothFont_actionPerformed(ActionEvent e)
2466 public void annotationColour_actionPerformed(ActionEvent e)
2471 public void rnahelicesColour_actionPerformed(ActionEvent e)
2476 public void associatedData_actionPerformed(ActionEvent e)
2481 public void autoCalculate_actionPerformed(ActionEvent e)
2486 public void sortByTreeOption_actionPerformed(ActionEvent e)
2491 public void showAllSeqs_actionPerformed(ActionEvent e)
2496 public void showAllColumns_actionPerformed(ActionEvent e)
2501 public void hideSelSequences_actionPerformed(ActionEvent e)
2506 public void hideSelColumns_actionPerformed(ActionEvent e)
2511 public void hiddenMarkers_actionPerformed(ActionEvent e)
2516 public void findPdbId_actionPerformed(ActionEvent e)
2521 public void enterPdbId_actionPerformed(ActionEvent e)
2526 public void pdbFile_actionPerformed(ActionEvent e)
2531 public void invertColSel_actionPerformed(ActionEvent e)
2536 public void tabSelectionChanged(int sel)
2541 public void tabbedPane_mousePressed(MouseEvent e)
2546 public void tabbedPane_focusGained(FocusEvent e)
2551 public void save_actionPerformed(ActionEvent e)
2556 public void reload_actionPerformed(ActionEvent e)
2561 public void newView_actionPerformed(ActionEvent e)
2566 public void textColour_actionPerformed(ActionEvent e)
2571 public void idRightAlign_actionPerformed(ActionEvent e)
2576 public void expandViews_actionPerformed(ActionEvent e)
2581 public void gatherViews_actionPerformed(ActionEvent e)
2586 public void buildTreeMenu()
2591 public void pageSetup_actionPerformed(ActionEvent e)
2596 public void alignmentProperties()