2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, 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;
21 import java.awt.event.*;
24 import javax.swing.event.*;
26 import jalview.schemes.*;
28 public class GAlignFrame extends JInternalFrame
30 protected JMenuBar alignFrameMenuBar = new JMenuBar();
32 protected JMenu fileMenu = new JMenu();
34 protected JMenuItem closeMenuItem = new JMenuItem();
36 protected JMenu editMenu = new JMenu();
38 protected JMenu viewMenu = new JMenu();
40 protected JMenu colourMenu = new JMenu();
42 protected JMenu calculateMenu = new JMenu();
44 protected JMenu webService = new JMenu();
46 protected JMenuItem webServiceNoServices;
48 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
50 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
52 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
54 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
56 protected JMenuItem remove2RightMenuItem = new JMenuItem();
58 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
60 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
62 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
64 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
66 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
68 protected JMenuItem sortIDMenuItem = new JMenuItem();
70 protected JMenuItem sortLengthMenuItem = new JMenuItem();
72 protected JMenuItem sortGroupMenuItem = new JMenuItem();
74 protected JMenu sortByAnnotScore = new JMenu();
76 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
78 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
80 protected JMenuItem PCAMenuItem = new JMenuItem();
82 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
84 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
86 BorderLayout borderLayout1 = new BorderLayout();
88 public JLabel statusBar = new JLabel();
90 protected JMenuItem saveAs = new JMenuItem();
92 protected JMenu outputTextboxMenu = new JMenu();
94 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
96 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
98 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
100 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
102 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
104 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
106 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
108 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
110 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
112 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
114 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
116 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
118 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
120 // protected JRadioButtonMenuItem covariationColour = new
121 // JRadioButtonMenuItem();
123 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
125 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
127 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
129 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
131 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
133 JMenuItem htmlMenuItem = new JMenuItem();
135 JMenuItem overviewMenuItem = new JMenuItem();
137 protected JMenuItem undoMenuItem = new JMenuItem();
139 protected JMenuItem redoMenuItem = new JMenuItem();
141 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
143 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
145 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
147 JMenuItem printMenuItem = new JMenuItem();
149 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
151 JMenuItem findMenuItem = new JMenuItem();
153 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
155 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
157 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
159 JMenuItem deleteGroups = new JMenuItem();
161 JMenuItem delete = new JMenuItem();
163 JMenuItem copy = new JMenuItem();
165 JMenuItem cut = new JMenuItem();
167 JMenu pasteMenu = new JMenu();
169 JMenuItem pasteNew = new JMenuItem();
171 JMenuItem pasteThis = new JMenuItem();
173 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
175 JMenuItem createPNG = new JMenuItem();
177 protected JMenuItem font = new JMenuItem();
179 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
181 JMenuItem epsFile = new JMenuItem();
183 JMenuItem LoadtreeMenuItem = new JMenuItem();
185 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
187 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
189 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
191 protected JMenuItem modifyPID = new JMenuItem();
193 protected JMenuItem modifyConservation = new JMenuItem();
195 protected JMenu sortByTreeMenu = new JMenu();
197 protected JMenu sort = new JMenu();
199 protected JMenu calculateTree = new JMenu();
201 JMenu jMenu2 = new JMenu();
203 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
205 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
207 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
209 protected ButtonGroup colours = new ButtonGroup();
211 JMenuItem vamsasStore = new JMenuItem();
213 protected JMenuItem showTranslation = new JMenuItem();
215 protected JMenuItem extractScores = new JMenuItem();
217 protected JMenu showProducts = new JMenu();
219 public JMenuItem featureSettings = new JMenuItem();
221 JMenuItem fetchSequence = new JMenuItem();
223 JMenuItem annotationColour = new JMenuItem();
225 protected JMenuItem rnahelicesColour = new JMenuItem();
227 JMenuItem associatedData = new JMenuItem();
229 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
231 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
233 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
235 JMenu addSequenceMenu = new JMenu();
237 JMenuItem addFromFile = new JMenuItem();
239 JMenuItem addFromText = new JMenuItem();
241 JMenuItem addFromURL = new JMenuItem();
243 JMenuItem exportAnnotations = new JMenuItem();
245 JMenuItem exportFeatures = new JMenuItem();
247 protected JPanel statusPanel = new JPanel();
249 GridLayout gridLayout1 = new GridLayout();
251 JMenu jMenu3 = new JMenu();
253 JMenuItem showAllSeqs = new JMenuItem();
255 JMenuItem showAllColumns = new JMenuItem();
257 JMenu hideMenu = new JMenu();
259 JMenuItem hideSelSequences = new JMenuItem();
261 JMenuItem hideSelColumns = new JMenuItem();
263 JMenuItem hideAllButSelection = new JMenuItem();
265 JMenuItem hideAllSelection = new JMenuItem();
267 JMenuItem showAllhidden = new JMenuItem();
269 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
271 JMenuItem invertColSel = new JMenuItem();
273 protected JTabbedPane tabbedPane = new JTabbedPane();
275 JMenuItem save = new JMenuItem();
277 protected JMenuItem reload = new JMenuItem();
279 JMenuItem newView = new JMenuItem();
281 JMenuItem textColour = new JMenuItem();
283 JMenu formatMenu = new JMenu();
285 JMenu selectMenu = new JMenu();
287 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
289 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
291 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
293 protected JMenuItem gatherViews = new JMenuItem();
295 protected JMenuItem expandViews = new JMenuItem();
297 JMenuItem pageSetup = new JMenuItem();
299 JMenuItem alignmentProperties = new JMenuItem();
301 JMenu tooltipSettingsMenu = new JMenu();
303 private JMenuItem justifyLeftMenuItem = new JMenuItem();
305 private JMenuItem justifyRightMenuItem = new JMenuItem();
307 JMenu autoAnnMenu = new JMenu();
309 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
311 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
313 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
315 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
317 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
319 private JMenuItem grpsFromSelection = new JMenuItem();
326 setJMenuBar(alignFrameMenuBar);
328 // dynamically fill save as menu with available formats
329 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
331 JMenuItem item = new JMenuItem(
332 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
334 item.addActionListener(new java.awt.event.ActionListener()
336 public void actionPerformed(ActionEvent e)
338 outputText_actionPerformed(e);
342 outputTextboxMenu.add(item);
344 } catch (Exception e)
348 if (!new jalview.util.Platform().isAMac())
350 closeMenuItem.setMnemonic('C');
351 outputTextboxMenu.setMnemonic('T');
352 undoMenuItem.setMnemonic('Z');
353 redoMenuItem.setMnemonic('0');
354 copy.setMnemonic('C');
355 cut.setMnemonic('U');
356 pasteMenu.setMnemonic('P');
357 reload.setMnemonic('R');
360 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
362 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
363 .getUserColourSchemes().keys();
365 while (userColours.hasMoreElements())
367 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
368 userColours.nextElement().toString());
369 radioItem.setName("USER_DEFINED");
370 radioItem.addMouseListener(new MouseAdapter()
372 public void mousePressed(MouseEvent evt)
374 if (evt.isControlDown()
375 || SwingUtilities.isRightMouseButton(evt))
377 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
379 int option = JOptionPane.showInternalConfirmDialog(
380 jalview.gui.Desktop.desktop,
381 "Remove from default list?",
382 "Remove user defined colour",
383 JOptionPane.YES_NO_OPTION);
384 if (option == JOptionPane.YES_OPTION)
386 jalview.gui.UserDefinedColours
387 .removeColourFromDefaults(radioItem.getText());
388 colourMenu.remove(radioItem);
392 radioItem.addActionListener(new ActionListener()
394 public void actionPerformed(ActionEvent evt)
396 userDefinedColour_actionPerformed(evt);
403 radioItem.addActionListener(new ActionListener()
405 public void actionPerformed(ActionEvent evt)
407 userDefinedColour_actionPerformed(evt);
410 colourMenu.insert(radioItem, 15);
411 colours.add(radioItem);
414 colours.add(noColourmenuItem);
415 colours.add(clustalColour);
416 colours.add(zappoColour);
417 colours.add(taylorColour);
418 colours.add(hydrophobicityColour);
419 colours.add(helixColour);
420 colours.add(strandColour);
421 colours.add(turnColour);
422 colours.add(buriedColour);
423 colours.add(userDefinedColour);
424 colours.add(PIDColour);
425 colours.add(BLOSUM62Colour);
426 colours.add(nucleotideColour);
427 colours.add(purinePyrimidineColour);
428 // colours.add(covariationColour);
430 setColourSelected(jalview.bin.Cache
431 .getDefault("DEFAULT_COLOUR", "None"));
435 public void setColourSelected(String defaultColour)
438 if (defaultColour != null)
440 int index = ColourSchemeProperty
441 .getColourIndexFromName(defaultColour);
445 case ColourSchemeProperty.CLUSTAL:
446 clustalColour.setSelected(true);
450 case ColourSchemeProperty.BLOSUM:
451 BLOSUM62Colour.setSelected(true);
455 case ColourSchemeProperty.PID:
456 PIDColour.setSelected(true);
460 case ColourSchemeProperty.ZAPPO:
461 zappoColour.setSelected(true);
465 case ColourSchemeProperty.TAYLOR:
466 taylorColour.setSelected(true);
469 case ColourSchemeProperty.HYDROPHOBIC:
470 hydrophobicityColour.setSelected(true);
474 case ColourSchemeProperty.HELIX:
475 helixColour.setSelected(true);
479 case ColourSchemeProperty.STRAND:
480 strandColour.setSelected(true);
484 case ColourSchemeProperty.TURN:
485 turnColour.setSelected(true);
489 case ColourSchemeProperty.BURIED:
490 buriedColour.setSelected(true);
494 case ColourSchemeProperty.NUCLEOTIDE:
495 nucleotideColour.setSelected(true);
499 case ColourSchemeProperty.PURINEPYRIMIDINE:
500 purinePyrimidineColour.setSelected(true);
504 * case ColourSchemeProperty.COVARIATION:
505 * covariationColour.setSelected(true);
509 case ColourSchemeProperty.USER_DEFINED:
510 userDefinedColour.setSelected(true);
513 case ColourSchemeProperty.NONE:
515 noColourmenuItem.setSelected(true);
523 private void jbInit() throws Exception
525 fileMenu.setText("File");
526 saveAs.setText("Save As...");
527 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
528 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
529 .getMenuShortcutKeyMask()
530 | java.awt.event.KeyEvent.SHIFT_MASK, false));
531 saveAs.addActionListener(new ActionListener()
533 public void actionPerformed(ActionEvent e)
535 saveAs_actionPerformed(e);
538 closeMenuItem.setText("Close");
539 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
540 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
541 .getMenuShortcutKeyMask(), false));
542 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
544 public void actionPerformed(ActionEvent e)
546 closeMenuItem_actionPerformed(false);
549 editMenu.setText("Edit");
550 viewMenu.setText("View");
551 colourMenu.setText("Colour");
552 calculateMenu.setText("Calculate");
553 webService.setText("Web Service");
554 selectAllSequenceMenuItem.setText("Select All");
555 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
556 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
557 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
558 selectAllSequenceMenuItem
559 .addActionListener(new java.awt.event.ActionListener()
561 public void actionPerformed(ActionEvent e)
563 selectAllSequenceMenuItem_actionPerformed(e);
566 deselectAllSequenceMenuItem.setText("Deselect All");
567 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
568 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
569 deselectAllSequenceMenuItem
570 .addActionListener(new java.awt.event.ActionListener()
572 public void actionPerformed(ActionEvent e)
574 deselectAllSequenceMenuItem_actionPerformed(e);
577 invertSequenceMenuItem.setText("Invert Sequence Selection");
578 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
579 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
580 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
581 invertSequenceMenuItem
582 .addActionListener(new java.awt.event.ActionListener()
584 public void actionPerformed(ActionEvent e)
586 invertSequenceMenuItem_actionPerformed(e);
589 grpsFromSelection.setText("Make Groups for selection");
590 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
592 public void actionPerformed(ActionEvent e)
594 makeGrpsFromSelection_actionPerformed(e);
598 remove2LeftMenuItem.setText("Remove Left");
599 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
600 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
601 .getMenuShortcutKeyMask(), false));
603 .addActionListener(new java.awt.event.ActionListener()
605 public void actionPerformed(ActionEvent e)
607 remove2LeftMenuItem_actionPerformed(e);
610 remove2RightMenuItem.setText("Remove Right");
611 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
612 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
613 .getMenuShortcutKeyMask(), false));
615 .addActionListener(new java.awt.event.ActionListener()
617 public void actionPerformed(ActionEvent e)
619 remove2RightMenuItem_actionPerformed(e);
622 removeGappedColumnMenuItem.setText("Remove Empty Columns");
623 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
624 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
625 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
626 removeGappedColumnMenuItem
627 .addActionListener(new java.awt.event.ActionListener()
629 public void actionPerformed(ActionEvent e)
631 removeGappedColumnMenuItem_actionPerformed(e);
634 removeAllGapsMenuItem.setText("Remove All Gaps");
635 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
636 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
637 .getDefaultToolkit().getMenuShortcutKeyMask()
638 | java.awt.event.KeyEvent.SHIFT_MASK, false));
639 removeAllGapsMenuItem
640 .addActionListener(new java.awt.event.ActionListener()
642 public void actionPerformed(ActionEvent e)
644 removeAllGapsMenuItem_actionPerformed(e);
647 justifyLeftMenuItem.setText("Left Justify Alignment");
649 .addActionListener(new java.awt.event.ActionListener()
651 public void actionPerformed(ActionEvent e)
653 justifyLeftMenuItem_actionPerformed(e);
656 justifyRightMenuItem.setText("Right Justify Alignment");
658 .addActionListener(new java.awt.event.ActionListener()
660 public void actionPerformed(ActionEvent e)
662 justifyRightMenuItem_actionPerformed(e);
665 viewBoxesMenuItem.setText("Boxes");
666 viewBoxesMenuItem.setState(true);
667 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
669 public void actionPerformed(ActionEvent e)
671 viewBoxesMenuItem_actionPerformed(e);
674 viewTextMenuItem.setText("Text");
675 viewTextMenuItem.setState(true);
676 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
678 public void actionPerformed(ActionEvent e)
680 viewTextMenuItem_actionPerformed(e);
683 showNonconservedMenuItem.setText("Show nonconserved");
684 showNonconservedMenuItem.setState(false);
685 showNonconservedMenuItem
686 .addActionListener(new java.awt.event.ActionListener()
688 public void actionPerformed(ActionEvent e)
690 showUnconservedMenuItem_actionPerformed(e);
693 sortPairwiseMenuItem.setText("by Pairwise Identity");
695 .addActionListener(new java.awt.event.ActionListener()
697 public void actionPerformed(ActionEvent e)
699 sortPairwiseMenuItem_actionPerformed(e);
702 sortIDMenuItem.setText("by ID");
703 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
705 public void actionPerformed(ActionEvent e)
707 sortIDMenuItem_actionPerformed(e);
710 sortLengthMenuItem.setText("By Length");
712 .addActionListener(new java.awt.event.ActionListener()
714 public void actionPerformed(ActionEvent e)
716 sortLengthMenuItem_actionPerformed(e);
719 sortGroupMenuItem.setText("by Group");
720 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
722 public void actionPerformed(ActionEvent e)
724 sortGroupMenuItem_actionPerformed(e);
727 removeRedundancyMenuItem.setText("Remove Redundancy...");
728 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
729 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
730 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
731 removeRedundancyMenuItem
732 .addActionListener(new java.awt.event.ActionListener()
734 public void actionPerformed(ActionEvent e)
736 removeRedundancyMenuItem_actionPerformed(e);
739 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
740 pairwiseAlignmentMenuItem
741 .addActionListener(new java.awt.event.ActionListener()
743 public void actionPerformed(ActionEvent e)
745 pairwiseAlignmentMenuItem_actionPerformed(e);
748 PCAMenuItem.setText("Principal Component Analysis");
749 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
751 public void actionPerformed(ActionEvent e)
753 PCAMenuItem_actionPerformed(e);
756 averageDistanceTreeMenuItem
757 .setText("Average Distance Using % Identity");
758 averageDistanceTreeMenuItem
759 .addActionListener(new java.awt.event.ActionListener()
761 public void actionPerformed(ActionEvent e)
763 averageDistanceTreeMenuItem_actionPerformed(e);
766 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
767 neighbourTreeMenuItem
768 .addActionListener(new java.awt.event.ActionListener()
770 public void actionPerformed(ActionEvent e)
772 neighbourTreeMenuItem_actionPerformed(e);
775 this.getContentPane().setLayout(borderLayout1);
776 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
777 statusBar.setBackground(Color.white);
778 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
779 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
780 statusBar.setText("Status bar");
781 outputTextboxMenu.setText("Output to Textbox");
782 clustalColour.setText("Clustalx");
784 clustalColour.addActionListener(new java.awt.event.ActionListener()
786 public void actionPerformed(ActionEvent e)
788 clustalColour_actionPerformed(e);
791 zappoColour.setText("Zappo");
792 zappoColour.addActionListener(new java.awt.event.ActionListener()
794 public void actionPerformed(ActionEvent e)
796 zappoColour_actionPerformed(e);
799 taylorColour.setText("Taylor");
800 taylorColour.addActionListener(new java.awt.event.ActionListener()
802 public void actionPerformed(ActionEvent e)
804 taylorColour_actionPerformed(e);
807 hydrophobicityColour.setText("Hydrophobicity");
809 .addActionListener(new java.awt.event.ActionListener()
811 public void actionPerformed(ActionEvent e)
813 hydrophobicityColour_actionPerformed(e);
816 helixColour.setText("Helix Propensity");
817 helixColour.addActionListener(new java.awt.event.ActionListener()
819 public void actionPerformed(ActionEvent e)
821 helixColour_actionPerformed(e);
824 strandColour.setText("Strand Propensity");
825 strandColour.addActionListener(new java.awt.event.ActionListener()
827 public void actionPerformed(ActionEvent e)
829 strandColour_actionPerformed(e);
832 turnColour.setText("Turn Propensity");
833 turnColour.addActionListener(new java.awt.event.ActionListener()
835 public void actionPerformed(ActionEvent e)
837 turnColour_actionPerformed(e);
840 buriedColour.setText("Buried Index");
841 buriedColour.addActionListener(new java.awt.event.ActionListener()
843 public void actionPerformed(ActionEvent e)
845 buriedColour_actionPerformed(e);
848 userDefinedColour.setText("User Defined...");
849 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
851 public void actionPerformed(ActionEvent e)
853 userDefinedColour_actionPerformed(e);
856 PIDColour.setText("Percentage Identity");
857 PIDColour.addActionListener(new java.awt.event.ActionListener()
859 public void actionPerformed(ActionEvent e)
861 PIDColour_actionPerformed(e);
864 BLOSUM62Colour.setText("BLOSUM62 Score");
865 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
867 public void actionPerformed(ActionEvent e)
869 BLOSUM62Colour_actionPerformed(e);
872 nucleotideColour.setText("Nucleotide");
873 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
875 public void actionPerformed(ActionEvent e)
877 nucleotideColour_actionPerformed(e);
881 purinePyrimidineColour.setText("Purine/Pyrimidine");
882 purinePyrimidineColour
883 .addActionListener(new java.awt.event.ActionListener()
885 public void actionPerformed(ActionEvent e)
887 purinePyrimidineColour_actionPerformed(e);
891 * covariationColour.setText("Covariation");
892 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
893 * public void actionPerformed(ActionEvent e) {
894 * covariationColour_actionPerformed(e); } });
897 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
898 avDistanceTreeBlosumMenuItem
899 .addActionListener(new java.awt.event.ActionListener()
901 public void actionPerformed(ActionEvent e)
903 avTreeBlosumMenuItem_actionPerformed(e);
906 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
908 .addActionListener(new java.awt.event.ActionListener()
910 public void actionPerformed(ActionEvent e)
912 njTreeBlosumMenuItem_actionPerformed(e);
915 annotationPanelMenuItem.setActionCommand("");
916 annotationPanelMenuItem.setText("Show Annotations");
917 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
918 "SHOW_ANNOTATIONS", true));
919 annotationPanelMenuItem
920 .addActionListener(new java.awt.event.ActionListener()
922 public void actionPerformed(ActionEvent e)
924 annotationPanelMenuItem_actionPerformed(e);
927 colourTextMenuItem.setText("Colour Text");
929 .addActionListener(new java.awt.event.ActionListener()
931 public void actionPerformed(ActionEvent e)
933 colourTextMenuItem_actionPerformed(e);
936 htmlMenuItem.setText("HTML");
937 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
939 public void actionPerformed(ActionEvent e)
941 htmlMenuItem_actionPerformed(e);
944 overviewMenuItem.setText("Overview Window");
945 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
947 public void actionPerformed(ActionEvent e)
949 overviewMenuItem_actionPerformed(e);
952 undoMenuItem.setEnabled(false);
953 undoMenuItem.setText("Undo");
954 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
955 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
956 .getMenuShortcutKeyMask(), false));
957 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
959 public void actionPerformed(ActionEvent e)
961 undoMenuItem_actionPerformed(e);
964 redoMenuItem.setEnabled(false);
965 redoMenuItem.setText("Redo");
966 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
967 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
968 .getMenuShortcutKeyMask(), false));
969 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
971 public void actionPerformed(ActionEvent e)
973 redoMenuItem_actionPerformed(e);
976 conservationMenuItem.setText("By Conservation");
978 .addActionListener(new java.awt.event.ActionListener()
980 public void actionPerformed(ActionEvent e)
982 conservationMenuItem_actionPerformed(e);
985 noColourmenuItem.setText("None");
986 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
988 public void actionPerformed(ActionEvent e)
990 noColourmenuItem_actionPerformed(e);
993 wrapMenuItem.setText("Wrap");
994 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
996 public void actionPerformed(ActionEvent e)
998 wrapMenuItem_actionPerformed(e);
1001 printMenuItem.setText("Print ...");
1002 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1003 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1004 .getMenuShortcutKeyMask(), false));
1005 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1007 public void actionPerformed(ActionEvent e)
1009 printMenuItem_actionPerformed(e);
1012 renderGapsMenuItem.setText("Show Gaps");
1013 renderGapsMenuItem.setState(true);
1015 .addActionListener(new java.awt.event.ActionListener()
1017 public void actionPerformed(ActionEvent e)
1019 renderGapsMenuItem_actionPerformed(e);
1022 findMenuItem.setText("Find...");
1023 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1024 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1025 .getMenuShortcutKeyMask(), false));
1026 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1028 public void actionPerformed(ActionEvent e)
1030 findMenuItem_actionPerformed(e);
1033 abovePIDThreshold.setText("Above Identity Threshold");
1034 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1036 public void actionPerformed(ActionEvent e)
1038 abovePIDThreshold_actionPerformed(e);
1041 showSeqFeatures.setText("Show Sequence Features");
1042 showSeqFeatures.addActionListener(new ActionListener()
1044 public void actionPerformed(ActionEvent actionEvent)
1046 showSeqFeatures_actionPerformed(actionEvent);
1050 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1051 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1052 * void actionPerformed(ActionEvent actionEvent) {
1053 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1055 showDbRefsMenuitem.setText("Show Database Refs");
1056 showDbRefsMenuitem.addActionListener(new ActionListener()
1059 public void actionPerformed(ActionEvent e)
1061 showDbRefs_actionPerformed(e);
1065 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1066 showNpFeatsMenuitem.addActionListener(new ActionListener()
1069 public void actionPerformed(ActionEvent e)
1071 showNpFeats_actionPerformed(e);
1075 showGroupConservation.setText("Group Conservation");
1076 showGroupConservation.addActionListener(new ActionListener()
1079 public void actionPerformed(ActionEvent e)
1081 showGroupConservation_actionPerformed(e);
1086 showGroupConsensus.setText("Group Consensus");
1087 showGroupConsensus.addActionListener(new ActionListener()
1090 public void actionPerformed(ActionEvent e)
1092 showGroupConsensus_actionPerformed(e);
1096 showConsensusHistogram.setText("Show Consensus Histogram");
1097 showConsensusHistogram.addActionListener(new ActionListener()
1100 public void actionPerformed(ActionEvent e)
1102 showConsensusHistogram_actionPerformed(e);
1106 showSequenceLogo.setText("Show Consensus Logo");
1107 showSequenceLogo.addActionListener(new ActionListener()
1110 public void actionPerformed(ActionEvent e)
1112 showSequenceLogo_actionPerformed(e);
1116 applyAutoAnnotationSettings.setText("Apply to all groups");
1117 applyAutoAnnotationSettings.setState(false);
1118 applyAutoAnnotationSettings.setVisible(true);
1119 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1122 public void actionPerformed(ActionEvent e)
1124 applyAutoAnnotationSettings_actionPerformed(e);
1129 nucleotideColour.setText("Nucleotide");
1130 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1132 public void actionPerformed(ActionEvent e)
1134 nucleotideColour_actionPerformed(e);
1137 deleteGroups.setText("Undefine groups");
1138 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1139 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1140 .getMenuShortcutKeyMask(), false));
1141 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1143 public void actionPerformed(ActionEvent e)
1145 deleteGroups_actionPerformed(e);
1148 copy.setText("Copy");
1149 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1150 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1151 .getMenuShortcutKeyMask(), false));
1153 copy.addActionListener(new java.awt.event.ActionListener()
1155 public void actionPerformed(ActionEvent e)
1157 copy_actionPerformed(e);
1161 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1162 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1163 .getMenuShortcutKeyMask(), false));
1164 cut.addActionListener(new java.awt.event.ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 cut_actionPerformed(e);
1171 delete.setText("Delete");
1172 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1173 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1174 delete.addActionListener(new java.awt.event.ActionListener()
1176 public void actionPerformed(ActionEvent e)
1178 delete_actionPerformed(e);
1181 pasteMenu.setText("Paste");
1182 pasteNew.setText("To New Alignment");
1183 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1184 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1185 .getMenuShortcutKeyMask()
1186 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1187 pasteNew.addActionListener(new java.awt.event.ActionListener()
1189 public void actionPerformed(ActionEvent e)
1191 pasteNew_actionPerformed(e);
1194 pasteThis.setText("Add To This Alignment");
1195 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1196 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1197 .getMenuShortcutKeyMask(), false));
1198 pasteThis.addActionListener(new java.awt.event.ActionListener()
1200 public void actionPerformed(ActionEvent e)
1202 pasteThis_actionPerformed(e);
1205 applyToAllGroups.setText("Apply Colour To All Groups");
1206 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1208 public void actionPerformed(ActionEvent e)
1210 applyToAllGroups_actionPerformed(e);
1213 createPNG.addActionListener(new java.awt.event.ActionListener()
1215 public void actionPerformed(ActionEvent e)
1220 createPNG.setActionCommand("Save As PNG Image");
1221 createPNG.setText("PNG");
1222 font.setText("Font...");
1223 font.addActionListener(new java.awt.event.ActionListener()
1225 public void actionPerformed(ActionEvent e)
1227 font_actionPerformed(e);
1231 seqLimits.setText("Show Sequence Limits");
1232 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1233 seqLimits.addActionListener(new java.awt.event.ActionListener()
1235 public void actionPerformed(ActionEvent e)
1237 seqLimit_actionPerformed(e);
1240 epsFile.setText("EPS");
1241 epsFile.addActionListener(new java.awt.event.ActionListener()
1243 public void actionPerformed(ActionEvent e)
1248 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1249 LoadtreeMenuItem.setText("Load Associated Tree");
1250 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1252 public void actionPerformed(ActionEvent e)
1254 LoadtreeMenuItem_actionPerformed(e);
1257 scaleAbove.setVisible(false);
1258 scaleAbove.setText("Scale Above");
1259 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1261 public void actionPerformed(ActionEvent e)
1263 scaleAbove_actionPerformed(e);
1266 scaleLeft.setVisible(false);
1267 scaleLeft.setSelected(true);
1268 scaleLeft.setText("Scale Left");
1269 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1271 public void actionPerformed(ActionEvent e)
1273 scaleLeft_actionPerformed(e);
1276 scaleRight.setVisible(false);
1277 scaleRight.setSelected(true);
1278 scaleRight.setText("Scale Right");
1279 scaleRight.addActionListener(new java.awt.event.ActionListener()
1281 public void actionPerformed(ActionEvent e)
1283 scaleRight_actionPerformed(e);
1286 centreColumnLabelsMenuItem.setVisible(true);
1287 centreColumnLabelsMenuItem.setState(false);
1288 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1289 centreColumnLabelsMenuItem
1290 .addActionListener(new java.awt.event.ActionListener()
1292 public void actionPerformed(ActionEvent e)
1294 centreColumnLabels_actionPerformed(e);
1297 followHighlightMenuItem.setVisible(true);
1298 followHighlightMenuItem.setState(true);
1299 followHighlightMenuItem.setText("Automatic Scrolling");
1300 followHighlightMenuItem.addActionListener(new ActionListener()
1303 public void actionPerformed(ActionEvent e)
1305 followHighlight_actionPerformed();
1310 modifyPID.setText("Modify Identity Threshold...");
1311 modifyPID.addActionListener(new java.awt.event.ActionListener()
1313 public void actionPerformed(ActionEvent e)
1315 modifyPID_actionPerformed(e);
1318 modifyConservation.setText("Modify Conservation Threshold...");
1320 .addActionListener(new java.awt.event.ActionListener()
1322 public void actionPerformed(ActionEvent e)
1324 modifyConservation_actionPerformed(e);
1327 sortByTreeMenu.setText("By Tree Order");
1328 sort.setText("Sort");
1329 sort.addMenuListener(new MenuListener()
1331 public void menuSelected(MenuEvent e)
1336 public void menuDeselected(MenuEvent e)
1340 public void menuCanceled(MenuEvent e)
1344 sortByAnnotScore.setText("by Score");
1345 sort.add(sortByAnnotScore);
1346 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1349 public void menuCanceled(MenuEvent e)
1353 public void menuDeselected(MenuEvent e)
1357 public void menuSelected(MenuEvent e)
1359 buildSortByAnnotationScoresMenu();
1362 sortByAnnotScore.setVisible(false);
1364 calculateTree.setText("Calculate Tree");
1366 jMenu2.setText("Export Image");
1367 padGapsMenuitem.setText("Pad Gaps");
1368 padGapsMenuitem.setState(jalview.bin.Cache
1369 .getDefault("PAD_GAPS", false));
1370 padGapsMenuitem.addActionListener(new ActionListener()
1372 public void actionPerformed(ActionEvent e)
1374 padGapsMenuitem_actionPerformed(e);
1377 vamsasStore.setVisible(false);
1378 vamsasStore.setText("VAMSAS store");
1379 vamsasStore.addActionListener(new ActionListener()
1381 public void actionPerformed(ActionEvent e)
1383 vamsasStore_actionPerformed(e);
1386 showTranslation.setText("Translate cDNA");
1387 showTranslation.addActionListener(new ActionListener()
1389 public void actionPerformed(ActionEvent e)
1391 showTranslation_actionPerformed(e);
1394 extractScores.setText("Extract Scores...");
1395 extractScores.addActionListener(new ActionListener()
1397 public void actionPerformed(ActionEvent e)
1399 extractScores_actionPerformed(e);
1402 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1404 showProducts.setText("Get Cross References");
1406 * showProducts.addActionListener(new ActionListener() {
1408 * public void actionPerformed(ActionEvent e) {
1409 * showProducts_actionPerformed(e); } });
1411 featureSettings.setText("Feature Settings...");
1412 featureSettings.addActionListener(new ActionListener()
1414 public void actionPerformed(ActionEvent e)
1416 featureSettings_actionPerformed(e);
1419 fetchSequence.setText("Fetch Sequence(s)...");
1420 fetchSequence.addActionListener(new ActionListener()
1422 public void actionPerformed(ActionEvent e)
1424 fetchSequence_actionPerformed(e);
1428 annotationColour.setText("By Annotation...");
1429 annotationColour.addActionListener(new ActionListener()
1431 public void actionPerformed(ActionEvent e)
1433 annotationColour_actionPerformed(e);
1437 rnahelicesColour.setText("By RNA helices");
1438 rnahelicesColour.addActionListener(new ActionListener()
1440 public void actionPerformed(ActionEvent e)
1442 rnahelicesColour_actionPerformed(e);
1446 associatedData.setText("Load Features / Annotations");
1447 associatedData.addActionListener(new ActionListener()
1449 public void actionPerformed(ActionEvent e)
1451 associatedData_actionPerformed(e);
1454 autoCalculate.setText("Autocalculate Consensus");
1455 autoCalculate.setState(jalview.bin.Cache.getDefault(
1456 "AUTO_CALC_CONSENSUS", true));
1457 autoCalculate.addActionListener(new ActionListener()
1459 public void actionPerformed(ActionEvent e)
1461 autoCalculate_actionPerformed(e);
1464 sortByTree.setText("Sort Alignment With New Tree");
1465 sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1466 sortByTree.setState(jalview.bin.Cache.getDefault(
1467 "SORT_BY_TREE", false));
1468 sortByTree.addActionListener(new ActionListener()
1470 public void actionPerformed(ActionEvent e)
1472 sortByTreeOption_actionPerformed(e);
1476 listenToViewSelections.setText("Listen for selections");
1477 listenToViewSelections.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1478 listenToViewSelections.setState(false);
1479 listenToViewSelections.addActionListener(new ActionListener()
1481 public void actionPerformed(ActionEvent e)
1483 listenToViewSelections_actionPerformed(e);
1487 addSequenceMenu.setText("Add Sequences");
1488 addFromFile.setText("From File");
1489 addFromFile.addActionListener(new ActionListener()
1491 public void actionPerformed(ActionEvent e)
1493 addFromFile_actionPerformed(e);
1496 addFromText.setText("From Textbox");
1497 addFromText.addActionListener(new ActionListener()
1499 public void actionPerformed(ActionEvent e)
1501 addFromText_actionPerformed(e);
1504 addFromURL.setText("From URL");
1505 addFromURL.addActionListener(new ActionListener()
1507 public void actionPerformed(ActionEvent e)
1509 addFromURL_actionPerformed(e);
1512 exportFeatures.setText("Export Features...");
1513 exportFeatures.addActionListener(new ActionListener()
1515 public void actionPerformed(ActionEvent e)
1517 exportFeatures_actionPerformed(e);
1520 exportAnnotations.setText("Export Annotations...");
1521 exportAnnotations.addActionListener(new ActionListener()
1523 public void actionPerformed(ActionEvent e)
1525 exportAnnotations_actionPerformed(e);
1528 statusPanel.setLayout(gridLayout1);
1529 jMenu3.setText("Show");
1530 showAllSeqs.setText("All Sequences");
1531 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1532 showAllSeqs.addActionListener(new ActionListener()
1534 public void actionPerformed(ActionEvent e)
1536 showAllSeqs_actionPerformed(e);
1539 showAllColumns.setText("All Columns");
1540 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1541 showAllColumns.addActionListener(new ActionListener()
1543 public void actionPerformed(ActionEvent e)
1545 showAllColumns_actionPerformed(e);
1548 hideMenu.setText("Hide");
1549 hideSelSequences.setText("Selected Sequences");
1550 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1551 hideSelSequences.addActionListener(new ActionListener()
1553 public void actionPerformed(ActionEvent e)
1555 hideSelSequences_actionPerformed(e);
1558 hideSelColumns.setText("Selected Columns");
1559 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1560 hideSelColumns.addActionListener(new ActionListener()
1562 public void actionPerformed(ActionEvent e)
1564 hideSelColumns_actionPerformed(e);
1567 hideAllSelection.setText("Selected Region");
1568 hideAllSelection.addActionListener(new ActionListener()
1570 public void actionPerformed(ActionEvent e)
1572 hideAllSelection_actionPerformed(e);
1575 // TODO: should be hidden if no selection exists.
1576 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1577 hideAllButSelection.addActionListener(new ActionListener()
1579 public void actionPerformed(ActionEvent e)
1581 hideAllButSelection_actionPerformed(e);
1584 showAllhidden.setText("All Sequences and Columns");
1586 .setToolTipText("H toggles visibility of hidden or selected regions.");
1587 showAllhidden.addActionListener(new ActionListener()
1589 public void actionPerformed(ActionEvent e)
1591 showAllhidden_actionPerformed(e);
1595 hiddenMarkers.setText("Show Hidden Markers");
1596 hiddenMarkers.addActionListener(new ActionListener()
1598 public void actionPerformed(ActionEvent e)
1600 hiddenMarkers_actionPerformed(e);
1603 invertColSel.setText("Invert Column Selection");
1604 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1605 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1606 .getMenuShortcutKeyMask()
1607 | java.awt.event.KeyEvent.ALT_MASK, false));
1608 invertColSel.addActionListener(new ActionListener()
1610 public void actionPerformed(ActionEvent e)
1612 invertColSel_actionPerformed(e);
1615 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1617 public void stateChanged(ChangeEvent evt)
1619 JTabbedPane pane = (JTabbedPane) evt.getSource();
1620 int sel = pane.getSelectedIndex();
1621 tabSelectionChanged(sel);
1624 tabbedPane.addMouseListener(new MouseAdapter()
1626 public void mousePressed(MouseEvent e)
1628 tabbedPane_mousePressed(e);
1631 tabbedPane.addFocusListener(new FocusAdapter()
1633 public void focusGained(FocusEvent e)
1635 tabbedPane_focusGained(e);
1638 save.setText("Save");
1639 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1640 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1641 .getMenuShortcutKeyMask(), false));
1642 save.addActionListener(new ActionListener()
1644 public void actionPerformed(ActionEvent e)
1646 save_actionPerformed(e);
1649 reload.setEnabled(false);
1650 reload.setText("Reload");
1651 reload.addActionListener(new ActionListener()
1653 public void actionPerformed(ActionEvent e)
1655 reload_actionPerformed(e);
1658 newView.setText("New View");
1659 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1660 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1661 .getMenuShortcutKeyMask(), false));
1662 newView.addActionListener(new ActionListener()
1664 public void actionPerformed(ActionEvent e)
1666 newView_actionPerformed(e);
1669 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1670 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1671 textColour.setText("Colour Text ...");
1672 textColour.addActionListener(new ActionListener()
1674 public void actionPerformed(ActionEvent e)
1676 textColour_actionPerformed(e);
1679 formatMenu.setText("Format");
1680 selectMenu.setText("Select");
1681 idRightAlign.setText("Right Align Sequence Id");
1682 idRightAlign.addActionListener(new ActionListener()
1684 public void actionPerformed(ActionEvent e)
1686 idRightAlign_actionPerformed(e);
1689 gatherViews.setEnabled(false);
1690 gatherViews.setText("Gather Views");
1691 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1692 java.awt.event.KeyEvent.VK_G, 0, false));
1693 gatherViews.addActionListener(new ActionListener()
1695 public void actionPerformed(ActionEvent e)
1697 gatherViews_actionPerformed(e);
1700 expandViews.setEnabled(false);
1701 expandViews.setText("Expand Views");
1702 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1703 java.awt.event.KeyEvent.VK_X, 0, false));
1704 expandViews.addActionListener(new ActionListener()
1706 public void actionPerformed(ActionEvent e)
1708 expandViews_actionPerformed(e);
1711 pageSetup.setText("Page Setup ...");
1712 pageSetup.addActionListener(new ActionListener()
1714 public void actionPerformed(ActionEvent e)
1716 pageSetup_actionPerformed(e);
1719 alignmentProperties.setText("Alignment Properties...");
1720 alignmentProperties.addActionListener(new ActionListener()
1722 public void actionPerformed(ActionEvent actionEvent)
1724 alignmentProperties();
1727 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1728 autoAnnMenu.setText("Autocalculated Annotation");
1729 alignFrameMenuBar.add(fileMenu);
1730 alignFrameMenuBar.add(editMenu);
1731 alignFrameMenuBar.add(selectMenu);
1732 alignFrameMenuBar.add(viewMenu);
1733 alignFrameMenuBar.add(formatMenu);
1734 alignFrameMenuBar.add(colourMenu);
1735 alignFrameMenuBar.add(calculateMenu);
1736 alignFrameMenuBar.add(webService);
1737 fileMenu.add(fetchSequence);
1738 fileMenu.add(addSequenceMenu);
1739 fileMenu.add(reload);
1740 fileMenu.addSeparator();
1741 fileMenu.add(vamsasStore);
1743 fileMenu.add(saveAs);
1744 fileMenu.add(outputTextboxMenu);
1745 fileMenu.add(pageSetup);
1746 fileMenu.add(printMenuItem);
1747 fileMenu.addSeparator();
1748 fileMenu.add(jMenu2);
1749 fileMenu.add(exportFeatures);
1750 fileMenu.add(exportAnnotations);
1751 fileMenu.add(LoadtreeMenuItem);
1752 fileMenu.add(associatedData);
1753 fileMenu.addSeparator();
1754 fileMenu.add(closeMenuItem);
1755 editMenu.add(undoMenuItem);
1756 editMenu.add(redoMenuItem);
1759 editMenu.add(pasteMenu);
1760 editMenu.add(delete);
1761 editMenu.addSeparator();
1762 editMenu.add(remove2LeftMenuItem);
1763 editMenu.add(remove2RightMenuItem);
1764 editMenu.add(removeGappedColumnMenuItem);
1765 editMenu.add(removeAllGapsMenuItem);
1766 editMenu.add(removeRedundancyMenuItem);
1767 editMenu.addSeparator();
1768 // dont add these yet in the CVS build - they cannot be undone!
1769 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1770 // editMenu.add(justifyLeftMenuItem);
1771 // editMenu.add(justifyRightMenuItem);
1772 // editMenu.addSeparator();
1773 editMenu.add(padGapsMenuitem);
1774 viewMenu.add(newView);
1775 viewMenu.add(expandViews);
1776 viewMenu.add(gatherViews);
1777 viewMenu.addSeparator();
1778 viewMenu.add(jMenu3);
1779 viewMenu.add(hideMenu);
1780 viewMenu.addSeparator();
1781 viewMenu.add(followHighlightMenuItem);
1782 viewMenu.add(annotationPanelMenuItem);
1783 autoAnnMenu.add(applyAutoAnnotationSettings);
1784 autoAnnMenu.add(showConsensusHistogram);
1785 autoAnnMenu.add(showSequenceLogo);
1786 autoAnnMenu.addSeparator();
1787 autoAnnMenu.add(showGroupConservation);
1788 autoAnnMenu.add(showGroupConsensus);
1789 viewMenu.add(autoAnnMenu);
1790 viewMenu.addSeparator();
1791 viewMenu.add(showSeqFeatures);
1792 // viewMenu.add(showSeqFeaturesHeight);
1794 viewMenu.add(featureSettings);
1795 tooltipSettingsMenu.add(showDbRefsMenuitem);
1796 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1797 viewMenu.add(tooltipSettingsMenu);
1798 viewMenu.addSeparator();
1799 viewMenu.add(alignmentProperties);
1800 viewMenu.addSeparator();
1801 viewMenu.add(overviewMenuItem);
1802 colourMenu.add(applyToAllGroups);
1803 colourMenu.add(textColour);
1804 colourMenu.addSeparator();
1805 colourMenu.add(noColourmenuItem);
1806 colourMenu.add(clustalColour);
1807 colourMenu.add(BLOSUM62Colour);
1808 colourMenu.add(PIDColour);
1809 colourMenu.add(zappoColour);
1810 colourMenu.add(taylorColour);
1811 colourMenu.add(hydrophobicityColour);
1812 colourMenu.add(helixColour);
1813 colourMenu.add(strandColour);
1814 colourMenu.add(turnColour);
1815 colourMenu.add(buriedColour);
1816 colourMenu.add(nucleotideColour);
1817 colourMenu.add(purinePyrimidineColour);
1818 // colourMenu.add(covariationColour);
1819 colourMenu.add(userDefinedColour);
1820 colourMenu.addSeparator();
1821 colourMenu.add(conservationMenuItem);
1822 colourMenu.add(modifyConservation);
1823 colourMenu.add(abovePIDThreshold);
1824 colourMenu.add(modifyPID);
1825 colourMenu.add(annotationColour);
1826 colourMenu.add(rnahelicesColour);
1827 calculateMenu.add(sort);
1828 calculateMenu.add(calculateTree);
1829 calculateMenu.addSeparator();
1830 calculateMenu.add(pairwiseAlignmentMenuItem);
1831 calculateMenu.add(PCAMenuItem);
1832 calculateMenu.addSeparator();
1833 calculateMenu.add(showTranslation);
1834 calculateMenu.add(showProducts);
1835 calculateMenu.add(autoCalculate);
1836 calculateMenu.add(sortByTree);
1837 calculateMenu.addSeparator();
1838 calculateMenu.add(extractScores);
1839 webServiceNoServices = new JMenuItem("<No Services>");
1840 webService.add(webServiceNoServices);
1841 pasteMenu.add(pasteNew);
1842 pasteMenu.add(pasteThis);
1843 sort.add(sortIDMenuItem);
1844 sort.add(sortLengthMenuItem);
1845 sort.add(sortGroupMenuItem);
1846 sort.add(sortPairwiseMenuItem);
1847 sort.add(sortByTreeMenu);
1848 calculateTree.add(averageDistanceTreeMenuItem);
1849 calculateTree.add(neighbourTreeMenuItem);
1850 calculateTree.add(avDistanceTreeBlosumMenuItem);
1851 calculateTree.add(njTreeBlosumMenuItem);
1852 jMenu2.add(htmlMenuItem);
1853 jMenu2.add(epsFile);
1854 jMenu2.add(createPNG);
1855 addSequenceMenu.add(addFromFile);
1856 addSequenceMenu.add(addFromText);
1857 addSequenceMenu.add(addFromURL);
1858 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1859 statusPanel.add(statusBar, null);
1860 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1861 jMenu3.add(showAllColumns);
1862 jMenu3.add(showAllSeqs);
1863 jMenu3.add(showAllhidden);
1864 hideMenu.add(hideSelColumns);
1865 hideMenu.add(hideSelSequences);
1866 hideMenu.add(hideAllSelection);
1867 hideMenu.add(hideAllButSelection);
1869 formatMenu.add(font);
1870 formatMenu.addSeparator();
1871 formatMenu.add(wrapMenuItem);
1872 formatMenu.add(scaleAbove);
1873 formatMenu.add(scaleLeft);
1874 formatMenu.add(scaleRight);
1875 formatMenu.add(seqLimits);
1876 formatMenu.add(idRightAlign);
1877 formatMenu.add(hiddenMarkers);
1878 formatMenu.add(viewBoxesMenuItem);
1879 formatMenu.add(viewTextMenuItem);
1880 formatMenu.add(colourTextMenuItem);
1881 formatMenu.add(renderGapsMenuItem);
1882 formatMenu.add(centreColumnLabelsMenuItem);
1883 formatMenu.add(showNonconservedMenuItem);
1884 selectMenu.add(findMenuItem);
1885 selectMenu.addSeparator();
1886 selectMenu.add(selectAllSequenceMenuItem);
1887 selectMenu.add(deselectAllSequenceMenuItem);
1888 selectMenu.add(invertSequenceMenuItem);
1889 selectMenu.add(invertColSel);
1890 selectMenu.add(deleteGroups);
1891 selectMenu.add(grpsFromSelection);
1892 // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
1893 //selectMenu.addSeparator();
1894 //selectMenu.add(listenToViewSelections);
1897 protected void listenToViewSelections_actionPerformed(ActionEvent e)
1899 // TODO Auto-generated method stub
1903 protected void showAllhidden_actionPerformed(ActionEvent e)
1905 // TODO Auto-generated method stub
1909 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1911 // TODO Auto-generated method stub
1915 protected void hideAllSelection_actionPerformed(ActionEvent e)
1917 // TODO Auto-generated method stub
1921 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1923 // TODO Auto-generated method stub
1927 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1929 // TODO Auto-generated method stub
1933 protected void showSequenceLogo_actionPerformed(ActionEvent e)
1935 // TODO Auto-generated method stub
1939 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1941 // TODO Auto-generated method stub
1945 protected void showGroupConsensus_actionPerformed(ActionEvent e)
1947 // TODO Auto-generated method stub
1951 protected void showGroupConservation_actionPerformed(ActionEvent e)
1953 // TODO Auto-generated method stub
1957 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1959 // TODO Auto-generated method stub
1963 protected void showSeqFeaturesHeight_actionPerformed(
1964 ActionEvent actionEvent)
1966 // TODO Auto-generated method stub
1970 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1972 // TODO Auto-generated method stub
1976 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1978 // TODO Auto-generated method stub
1982 protected void followHighlight_actionPerformed()
1984 // TODO Auto-generated method stub
1988 protected void showNpFeats_actionPerformed(ActionEvent e)
1990 // TODO Auto-generated method stub
1994 protected void showDbRefs_actionPerformed(ActionEvent e)
1996 // TODO Auto-generated method stub
2000 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2004 protected void showProducts_actionPerformed(ActionEvent e)
2008 protected void buildSortByAnnotationScoresMenu()
2012 protected void extractScores_actionPerformed(ActionEvent e)
2016 protected void outputText_actionPerformed(ActionEvent e)
2020 public void addFromFile_actionPerformed(ActionEvent e)
2025 public void addFromText_actionPerformed(ActionEvent e)
2030 public void addFromURL_actionPerformed(ActionEvent e)
2035 public void exportFeatures_actionPerformed(ActionEvent e)
2040 public void exportAnnotations_actionPerformed(ActionEvent e)
2045 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2049 protected void closeMenuItem_actionPerformed(boolean b)
2053 protected void redoMenuItem_actionPerformed(ActionEvent e)
2057 protected void undoMenuItem_actionPerformed(ActionEvent e)
2061 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2065 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2069 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2073 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2077 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2081 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2085 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2089 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2093 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2097 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2101 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2105 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2109 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2113 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2117 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2121 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2125 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2129 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2133 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2137 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2141 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2145 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2149 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2153 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2157 protected void clustalColour_actionPerformed(ActionEvent e)
2161 protected void zappoColour_actionPerformed(ActionEvent e)
2165 protected void taylorColour_actionPerformed(ActionEvent e)
2169 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2173 protected void helixColour_actionPerformed(ActionEvent e)
2177 protected void strandColour_actionPerformed(ActionEvent e)
2181 protected void turnColour_actionPerformed(ActionEvent e)
2185 protected void buriedColour_actionPerformed(ActionEvent e)
2189 protected void userDefinedColour_actionPerformed(ActionEvent e)
2193 protected void PIDColour_actionPerformed(ActionEvent e)
2197 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2201 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2206 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2209 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2213 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2217 protected void printMenuItem_actionPerformed(ActionEvent e)
2221 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2225 protected void findMenuItem_actionPerformed(ActionEvent e)
2229 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2233 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2237 protected void nucleotideColour_actionPerformed(ActionEvent e)
2241 protected void deleteGroups_actionPerformed(ActionEvent e)
2245 protected void copy_actionPerformed(ActionEvent e)
2249 protected void cut_actionPerformed(ActionEvent e)
2253 protected void delete_actionPerformed(ActionEvent e)
2257 protected void pasteNew_actionPerformed(ActionEvent e)
2261 protected void pasteThis_actionPerformed(ActionEvent e)
2265 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2269 public void createPNG(java.io.File f)
2273 protected void font_actionPerformed(ActionEvent e)
2277 protected void seqLimit_actionPerformed(ActionEvent e)
2281 public void seqDBRef_actionPerformed(ActionEvent e)
2286 public void createEPS(java.io.File f)
2290 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2294 protected void jpred_actionPerformed(ActionEvent e)
2298 protected void scaleAbove_actionPerformed(ActionEvent e)
2302 protected void scaleLeft_actionPerformed(ActionEvent e)
2306 protected void scaleRight_actionPerformed(ActionEvent e)
2310 protected void modifyPID_actionPerformed(ActionEvent e)
2314 protected void modifyConservation_actionPerformed(ActionEvent e)
2318 protected void saveAs_actionPerformed(ActionEvent e)
2322 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2326 public void vamsasStore_actionPerformed(ActionEvent e)
2331 public void vamsasLoad_actionPerformed(ActionEvent e)
2336 public void showTranslation_actionPerformed(ActionEvent e)
2341 public void featureSettings_actionPerformed(ActionEvent e)
2346 public void fetchSequence_actionPerformed(ActionEvent e)
2351 public void smoothFont_actionPerformed(ActionEvent e)
2356 public void annotationColour_actionPerformed(ActionEvent e)
2361 public void rnahelicesColour_actionPerformed(ActionEvent e)
2366 public void associatedData_actionPerformed(ActionEvent e)
2371 public void autoCalculate_actionPerformed(ActionEvent e)
2376 public void sortByTreeOption_actionPerformed(ActionEvent e)
2381 public void showAllSeqs_actionPerformed(ActionEvent e)
2386 public void showAllColumns_actionPerformed(ActionEvent e)
2391 public void hideSelSequences_actionPerformed(ActionEvent e)
2396 public void hideSelColumns_actionPerformed(ActionEvent e)
2401 public void hiddenMarkers_actionPerformed(ActionEvent e)
2406 public void findPdbId_actionPerformed(ActionEvent e)
2411 public void enterPdbId_actionPerformed(ActionEvent e)
2416 public void pdbFile_actionPerformed(ActionEvent e)
2421 public void invertColSel_actionPerformed(ActionEvent e)
2426 public void tabSelectionChanged(int sel)
2431 public void tabbedPane_mousePressed(MouseEvent e)
2436 public void tabbedPane_focusGained(FocusEvent e)
2441 public void save_actionPerformed(ActionEvent e)
2446 public void reload_actionPerformed(ActionEvent e)
2451 public void newView_actionPerformed(ActionEvent e)
2456 public void textColour_actionPerformed(ActionEvent e)
2461 public void idRightAlign_actionPerformed(ActionEvent e)
2466 public void expandViews_actionPerformed(ActionEvent e)
2471 public void gatherViews_actionPerformed(ActionEvent e)
2476 public void buildTreeMenu()
2481 public void pageSetup_actionPerformed(ActionEvent e)
2486 public void alignmentProperties()