2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 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 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
118 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
120 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
122 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
124 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
126 JMenuItem htmlMenuItem = new JMenuItem();
128 JMenuItem overviewMenuItem = new JMenuItem();
130 protected JMenuItem undoMenuItem = new JMenuItem();
132 protected JMenuItem redoMenuItem = new JMenuItem();
134 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
136 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
138 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
140 JMenuItem printMenuItem = new JMenuItem();
142 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
144 JMenuItem findMenuItem = new JMenuItem();
146 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
148 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
150 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
152 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
154 JMenuItem deleteGroups = new JMenuItem();
156 JMenuItem delete = new JMenuItem();
158 JMenuItem copy = new JMenuItem();
160 JMenuItem cut = new JMenuItem();
162 JMenu pasteMenu = new JMenu();
164 JMenuItem pasteNew = new JMenuItem();
166 JMenuItem pasteThis = new JMenuItem();
168 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
170 JMenuItem createPNG = new JMenuItem();
172 protected JMenuItem font = new JMenuItem();
174 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
176 JMenuItem epsFile = new JMenuItem();
178 JMenuItem LoadtreeMenuItem = new JMenuItem();
180 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
182 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
184 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
186 protected JMenuItem modifyPID = new JMenuItem();
188 protected JMenuItem modifyConservation = new JMenuItem();
190 protected JMenu sortByTreeMenu = new JMenu();
192 protected JMenu sort = new JMenu();
194 protected JMenu calculateTree = new JMenu();
196 JMenu jMenu2 = new JMenu();
198 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
200 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
202 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
204 protected ButtonGroup colours = new ButtonGroup();
206 JMenuItem vamsasStore = new JMenuItem();
208 protected JMenuItem showTranslation = new JMenuItem();
210 protected JMenuItem extractScores = new JMenuItem();
212 protected JMenu showProducts = new JMenu();
214 public JMenuItem featureSettings = new JMenuItem();
216 JMenuItem fetchSequence = new JMenuItem();
218 JMenuItem annotationColour = new JMenuItem();
220 JMenuItem associatedData = new JMenuItem();
222 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
224 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
226 JMenu addSequenceMenu = new JMenu();
228 JMenuItem addFromFile = new JMenuItem();
230 JMenuItem addFromText = new JMenuItem();
232 JMenuItem addFromURL = new JMenuItem();
234 JMenuItem exportAnnotations = new JMenuItem();
236 JMenuItem exportFeatures = new JMenuItem();
238 protected JPanel statusPanel = new JPanel();
240 GridLayout gridLayout1 = new GridLayout();
242 JMenu jMenu3 = new JMenu();
244 JMenuItem showAllSeqs = new JMenuItem();
246 JMenuItem showAllColumns = new JMenuItem();
248 JMenu hideMenu = new JMenu();
250 JMenuItem hideSelSequences = new JMenuItem();
252 JMenuItem hideSelColumns = new JMenuItem();
254 JMenuItem hideAllButSelection = new JMenuItem();
256 JMenuItem hideAllSelection = new JMenuItem();
258 JMenuItem showAllhidden = new JMenuItem();
260 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
262 JMenuItem invertColSel = new JMenuItem();
264 protected JTabbedPane tabbedPane = new JTabbedPane();
266 JMenuItem save = new JMenuItem();
268 protected JMenuItem reload = new JMenuItem();
270 JMenuItem newView = new JMenuItem();
272 JMenuItem textColour = new JMenuItem();
274 JMenu formatMenu = new JMenu();
276 JMenu selectMenu = new JMenu();
278 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
280 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
282 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
284 protected JMenuItem gatherViews = new JMenuItem();
286 protected JMenuItem expandViews = new JMenuItem();
288 JMenuItem pageSetup = new JMenuItem();
290 JMenuItem alignmentProperties = new JMenuItem();
292 JMenu tooltipSettingsMenu = new JMenu();
294 private JMenuItem justifyLeftMenuItem = new JMenuItem();
296 private JMenuItem justifyRightMenuItem = new JMenuItem();
298 JMenu autoAnnMenu = new JMenu();
300 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
302 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
304 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
306 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
308 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
310 private JMenuItem grpsFromSelection = new JMenuItem();
317 setJMenuBar(alignFrameMenuBar);
319 // dynamically fill save as menu with available formats
320 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
322 JMenuItem item = new JMenuItem(
323 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
325 item.addActionListener(new java.awt.event.ActionListener()
327 public void actionPerformed(ActionEvent e)
329 outputText_actionPerformed(e);
333 outputTextboxMenu.add(item);
335 } catch (Exception e)
339 if (!new jalview.util.Platform().isAMac())
341 closeMenuItem.setMnemonic('C');
342 outputTextboxMenu.setMnemonic('T');
343 undoMenuItem.setMnemonic('Z');
344 redoMenuItem.setMnemonic('0');
345 copy.setMnemonic('C');
346 cut.setMnemonic('U');
347 pasteMenu.setMnemonic('P');
348 reload.setMnemonic('R');
351 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
353 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
354 .getUserColourSchemes().keys();
356 while (userColours.hasMoreElements())
358 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
359 userColours.nextElement().toString());
360 radioItem.setName("USER_DEFINED");
361 radioItem.addMouseListener(new MouseAdapter()
363 public void mousePressed(MouseEvent evt)
365 if (evt.isControlDown()
366 || SwingUtilities.isRightMouseButton(evt))
368 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
370 int option = JOptionPane.showInternalConfirmDialog(
371 jalview.gui.Desktop.desktop,
372 "Remove from default list?",
373 "Remove user defined colour",
374 JOptionPane.YES_NO_OPTION);
375 if (option == JOptionPane.YES_OPTION)
377 jalview.gui.UserDefinedColours
378 .removeColourFromDefaults(radioItem.getText());
379 colourMenu.remove(radioItem);
383 radioItem.addActionListener(new ActionListener()
385 public void actionPerformed(ActionEvent evt)
387 userDefinedColour_actionPerformed(evt);
394 radioItem.addActionListener(new ActionListener()
396 public void actionPerformed(ActionEvent evt)
398 userDefinedColour_actionPerformed(evt);
401 colourMenu.insert(radioItem, 15);
402 colours.add(radioItem);
405 colours.add(noColourmenuItem);
406 colours.add(clustalColour);
407 colours.add(zappoColour);
408 colours.add(taylorColour);
409 colours.add(hydrophobicityColour);
410 colours.add(helixColour);
411 colours.add(strandColour);
412 colours.add(turnColour);
413 colours.add(buriedColour);
414 colours.add(userDefinedColour);
415 colours.add(PIDColour);
416 colours.add(BLOSUM62Colour);
417 colours.add(nucleotideColour);
419 setColourSelected(jalview.bin.Cache
420 .getDefault("DEFAULT_COLOUR", "None"));
424 public void setColourSelected(String defaultColour)
427 if (defaultColour != null)
429 int index = ColourSchemeProperty
430 .getColourIndexFromName(defaultColour);
434 case ColourSchemeProperty.CLUSTAL:
435 clustalColour.setSelected(true);
439 case ColourSchemeProperty.BLOSUM:
440 BLOSUM62Colour.setSelected(true);
444 case ColourSchemeProperty.PID:
445 PIDColour.setSelected(true);
449 case ColourSchemeProperty.ZAPPO:
450 zappoColour.setSelected(true);
454 case ColourSchemeProperty.TAYLOR:
455 taylorColour.setSelected(true);
458 case ColourSchemeProperty.HYDROPHOBIC:
459 hydrophobicityColour.setSelected(true);
463 case ColourSchemeProperty.HELIX:
464 helixColour.setSelected(true);
468 case ColourSchemeProperty.STRAND:
469 strandColour.setSelected(true);
473 case ColourSchemeProperty.TURN:
474 turnColour.setSelected(true);
478 case ColourSchemeProperty.BURIED:
479 buriedColour.setSelected(true);
483 case ColourSchemeProperty.NUCLEOTIDE:
484 nucleotideColour.setSelected(true);
488 case ColourSchemeProperty.USER_DEFINED:
489 userDefinedColour.setSelected(true);
492 case ColourSchemeProperty.NONE:
494 noColourmenuItem.setSelected(true);
502 private void jbInit() throws Exception
504 fileMenu.setText("File");
505 saveAs.setText("Save As...");
506 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
507 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
508 .getMenuShortcutKeyMask()
509 | java.awt.event.KeyEvent.SHIFT_MASK, false));
510 saveAs.addActionListener(new ActionListener()
512 public void actionPerformed(ActionEvent e)
514 saveAs_actionPerformed(e);
517 closeMenuItem.setText("Close");
518 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
519 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
520 .getMenuShortcutKeyMask(), false));
521 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
523 public void actionPerformed(ActionEvent e)
525 closeMenuItem_actionPerformed(false);
528 editMenu.setText("Edit");
529 viewMenu.setText("View");
530 colourMenu.setText("Colour");
531 calculateMenu.setText("Calculate");
532 webService.setText("Web Service");
533 selectAllSequenceMenuItem.setText("Select All");
534 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
535 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
536 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
537 selectAllSequenceMenuItem
538 .addActionListener(new java.awt.event.ActionListener()
540 public void actionPerformed(ActionEvent e)
542 selectAllSequenceMenuItem_actionPerformed(e);
545 deselectAllSequenceMenuItem.setText("Deselect All");
546 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
547 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
548 deselectAllSequenceMenuItem
549 .addActionListener(new java.awt.event.ActionListener()
551 public void actionPerformed(ActionEvent e)
553 deselectAllSequenceMenuItem_actionPerformed(e);
556 invertSequenceMenuItem.setText("Invert Sequence Selection");
557 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
558 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
559 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
560 invertSequenceMenuItem
561 .addActionListener(new java.awt.event.ActionListener()
563 public void actionPerformed(ActionEvent e)
565 invertSequenceMenuItem_actionPerformed(e);
568 grpsFromSelection.setText("Make Groups for selection");
569 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
571 public void actionPerformed(ActionEvent e)
573 makeGrpsFromSelection_actionPerformed(e);
577 remove2LeftMenuItem.setText("Remove Left");
578 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
579 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
580 .getMenuShortcutKeyMask(), false));
582 .addActionListener(new java.awt.event.ActionListener()
584 public void actionPerformed(ActionEvent e)
586 remove2LeftMenuItem_actionPerformed(e);
589 remove2RightMenuItem.setText("Remove Right");
590 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
591 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
592 .getMenuShortcutKeyMask(), false));
594 .addActionListener(new java.awt.event.ActionListener()
596 public void actionPerformed(ActionEvent e)
598 remove2RightMenuItem_actionPerformed(e);
601 removeGappedColumnMenuItem.setText("Remove Empty Columns");
602 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
603 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
604 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
605 removeGappedColumnMenuItem
606 .addActionListener(new java.awt.event.ActionListener()
608 public void actionPerformed(ActionEvent e)
610 removeGappedColumnMenuItem_actionPerformed(e);
613 removeAllGapsMenuItem.setText("Remove All Gaps");
614 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
615 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
616 .getDefaultToolkit().getMenuShortcutKeyMask()
617 | java.awt.event.KeyEvent.SHIFT_MASK, false));
618 removeAllGapsMenuItem
619 .addActionListener(new java.awt.event.ActionListener()
621 public void actionPerformed(ActionEvent e)
623 removeAllGapsMenuItem_actionPerformed(e);
626 justifyLeftMenuItem.setText("Left Justify Alignment");
628 .addActionListener(new java.awt.event.ActionListener()
630 public void actionPerformed(ActionEvent e)
632 justifyLeftMenuItem_actionPerformed(e);
635 justifyRightMenuItem.setText("Right Justify Alignment");
637 .addActionListener(new java.awt.event.ActionListener()
639 public void actionPerformed(ActionEvent e)
641 justifyRightMenuItem_actionPerformed(e);
644 viewBoxesMenuItem.setText("Boxes");
645 viewBoxesMenuItem.setState(true);
646 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
648 public void actionPerformed(ActionEvent e)
650 viewBoxesMenuItem_actionPerformed(e);
653 viewTextMenuItem.setText("Text");
654 viewTextMenuItem.setState(true);
655 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
657 public void actionPerformed(ActionEvent e)
659 viewTextMenuItem_actionPerformed(e);
662 showNonconservedMenuItem.setText("Show nonconserved");
663 showNonconservedMenuItem.setState(false);
664 showNonconservedMenuItem
665 .addActionListener(new java.awt.event.ActionListener()
667 public void actionPerformed(ActionEvent e)
669 showUnconservedMenuItem_actionPerformed(e);
672 sortPairwiseMenuItem.setText("by Pairwise Identity");
674 .addActionListener(new java.awt.event.ActionListener()
676 public void actionPerformed(ActionEvent e)
678 sortPairwiseMenuItem_actionPerformed(e);
681 sortIDMenuItem.setText("by ID");
682 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
684 public void actionPerformed(ActionEvent e)
686 sortIDMenuItem_actionPerformed(e);
689 sortLengthMenuItem.setText("By Length");
691 .addActionListener(new java.awt.event.ActionListener()
693 public void actionPerformed(ActionEvent e)
695 sortLengthMenuItem_actionPerformed(e);
698 sortGroupMenuItem.setText("by Group");
699 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
701 public void actionPerformed(ActionEvent e)
703 sortGroupMenuItem_actionPerformed(e);
706 removeRedundancyMenuItem.setText("Remove Redundancy...");
707 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
708 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
709 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
710 removeRedundancyMenuItem
711 .addActionListener(new java.awt.event.ActionListener()
713 public void actionPerformed(ActionEvent e)
715 removeRedundancyMenuItem_actionPerformed(e);
718 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
719 pairwiseAlignmentMenuItem
720 .addActionListener(new java.awt.event.ActionListener()
722 public void actionPerformed(ActionEvent e)
724 pairwiseAlignmentMenuItem_actionPerformed(e);
727 PCAMenuItem.setText("Principal Component Analysis");
728 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
730 public void actionPerformed(ActionEvent e)
732 PCAMenuItem_actionPerformed(e);
735 averageDistanceTreeMenuItem
736 .setText("Average Distance Using % Identity");
737 averageDistanceTreeMenuItem
738 .addActionListener(new java.awt.event.ActionListener()
740 public void actionPerformed(ActionEvent e)
742 averageDistanceTreeMenuItem_actionPerformed(e);
745 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
746 neighbourTreeMenuItem
747 .addActionListener(new java.awt.event.ActionListener()
749 public void actionPerformed(ActionEvent e)
751 neighbourTreeMenuItem_actionPerformed(e);
754 this.getContentPane().setLayout(borderLayout1);
755 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
756 statusBar.setBackground(Color.white);
757 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
758 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
759 statusBar.setText("Status bar");
760 outputTextboxMenu.setText("Output to Textbox");
761 clustalColour.setText("Clustalx");
763 clustalColour.addActionListener(new java.awt.event.ActionListener()
765 public void actionPerformed(ActionEvent e)
767 clustalColour_actionPerformed(e);
770 zappoColour.setText("Zappo");
771 zappoColour.addActionListener(new java.awt.event.ActionListener()
773 public void actionPerformed(ActionEvent e)
775 zappoColour_actionPerformed(e);
778 taylorColour.setText("Taylor");
779 taylorColour.addActionListener(new java.awt.event.ActionListener()
781 public void actionPerformed(ActionEvent e)
783 taylorColour_actionPerformed(e);
786 hydrophobicityColour.setText("Hydrophobicity");
788 .addActionListener(new java.awt.event.ActionListener()
790 public void actionPerformed(ActionEvent e)
792 hydrophobicityColour_actionPerformed(e);
795 helixColour.setText("Helix Propensity");
796 helixColour.addActionListener(new java.awt.event.ActionListener()
798 public void actionPerformed(ActionEvent e)
800 helixColour_actionPerformed(e);
803 strandColour.setText("Strand Propensity");
804 strandColour.addActionListener(new java.awt.event.ActionListener()
806 public void actionPerformed(ActionEvent e)
808 strandColour_actionPerformed(e);
811 turnColour.setText("Turn Propensity");
812 turnColour.addActionListener(new java.awt.event.ActionListener()
814 public void actionPerformed(ActionEvent e)
816 turnColour_actionPerformed(e);
819 buriedColour.setText("Buried Index");
820 buriedColour.addActionListener(new java.awt.event.ActionListener()
822 public void actionPerformed(ActionEvent e)
824 buriedColour_actionPerformed(e);
827 userDefinedColour.setText("User Defined...");
828 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
830 public void actionPerformed(ActionEvent e)
832 userDefinedColour_actionPerformed(e);
835 PIDColour.setText("Percentage Identity");
836 PIDColour.addActionListener(new java.awt.event.ActionListener()
838 public void actionPerformed(ActionEvent e)
840 PIDColour_actionPerformed(e);
843 BLOSUM62Colour.setText("BLOSUM62 Score");
844 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
846 public void actionPerformed(ActionEvent e)
848 BLOSUM62Colour_actionPerformed(e);
851 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
852 avDistanceTreeBlosumMenuItem
853 .addActionListener(new java.awt.event.ActionListener()
855 public void actionPerformed(ActionEvent e)
857 avTreeBlosumMenuItem_actionPerformed(e);
860 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
862 .addActionListener(new java.awt.event.ActionListener()
864 public void actionPerformed(ActionEvent e)
866 njTreeBlosumMenuItem_actionPerformed(e);
869 annotationPanelMenuItem.setActionCommand("");
870 annotationPanelMenuItem.setText("Show Annotations");
871 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
872 "SHOW_ANNOTATIONS", true));
873 annotationPanelMenuItem
874 .addActionListener(new java.awt.event.ActionListener()
876 public void actionPerformed(ActionEvent e)
878 annotationPanelMenuItem_actionPerformed(e);
881 colourTextMenuItem.setText("Colour Text");
883 .addActionListener(new java.awt.event.ActionListener()
885 public void actionPerformed(ActionEvent e)
887 colourTextMenuItem_actionPerformed(e);
890 htmlMenuItem.setText("HTML");
891 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
893 public void actionPerformed(ActionEvent e)
895 htmlMenuItem_actionPerformed(e);
898 overviewMenuItem.setText("Overview Window");
899 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
901 public void actionPerformed(ActionEvent e)
903 overviewMenuItem_actionPerformed(e);
906 undoMenuItem.setEnabled(false);
907 undoMenuItem.setText("Undo");
908 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
909 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
910 .getMenuShortcutKeyMask(), false));
911 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
913 public void actionPerformed(ActionEvent e)
915 undoMenuItem_actionPerformed(e);
918 redoMenuItem.setEnabled(false);
919 redoMenuItem.setText("Redo");
920 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
921 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
922 .getMenuShortcutKeyMask(), false));
923 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
925 public void actionPerformed(ActionEvent e)
927 redoMenuItem_actionPerformed(e);
930 conservationMenuItem.setText("By Conservation");
932 .addActionListener(new java.awt.event.ActionListener()
934 public void actionPerformed(ActionEvent e)
936 conservationMenuItem_actionPerformed(e);
939 noColourmenuItem.setText("None");
940 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
942 public void actionPerformed(ActionEvent e)
944 noColourmenuItem_actionPerformed(e);
947 wrapMenuItem.setText("Wrap");
948 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
950 public void actionPerformed(ActionEvent e)
952 wrapMenuItem_actionPerformed(e);
955 printMenuItem.setText("Print ...");
956 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
957 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
958 .getMenuShortcutKeyMask(), false));
959 printMenuItem.addActionListener(new java.awt.event.ActionListener()
961 public void actionPerformed(ActionEvent e)
963 printMenuItem_actionPerformed(e);
966 renderGapsMenuItem.setText("Show Gaps");
967 renderGapsMenuItem.setState(true);
969 .addActionListener(new java.awt.event.ActionListener()
971 public void actionPerformed(ActionEvent e)
973 renderGapsMenuItem_actionPerformed(e);
976 findMenuItem.setText("Find...");
977 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
978 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
979 .getMenuShortcutKeyMask(), false));
980 findMenuItem.addActionListener(new java.awt.event.ActionListener()
982 public void actionPerformed(ActionEvent e)
984 findMenuItem_actionPerformed(e);
987 abovePIDThreshold.setText("Above Identity Threshold");
988 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
990 public void actionPerformed(ActionEvent e)
992 abovePIDThreshold_actionPerformed(e);
995 showSeqFeatures.setText("Show Sequence Features");
996 showSeqFeatures.addActionListener(new ActionListener()
998 public void actionPerformed(ActionEvent actionEvent)
1000 showSeqFeatures_actionPerformed(actionEvent);
1004 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1005 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1006 * void actionPerformed(ActionEvent actionEvent) {
1007 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1009 showDbRefsMenuitem.setText("Show Database Refs");
1010 showDbRefsMenuitem.addActionListener(new ActionListener()
1013 public void actionPerformed(ActionEvent e)
1015 showDbRefs_actionPerformed(e);
1019 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1020 showNpFeatsMenuitem.addActionListener(new ActionListener()
1023 public void actionPerformed(ActionEvent e)
1025 showNpFeats_actionPerformed(e);
1029 showGroupConservation.setText("Group Conservation");
1030 showGroupConservation.addActionListener(new ActionListener()
1033 public void actionPerformed(ActionEvent e)
1035 showGroupConservation_actionPerformed(e);
1040 showGroupConsensus.setText("Group Consensus");
1041 showGroupConsensus.addActionListener(new ActionListener()
1044 public void actionPerformed(ActionEvent e)
1046 showGroupConsensus_actionPerformed(e);
1050 showConsensusHistogram.setText("Show Consensus Histogram");
1051 showConsensusHistogram.addActionListener(new ActionListener()
1054 public void actionPerformed(ActionEvent e)
1056 showConsensusHistogram_actionPerformed(e);
1060 showSequenceLogo.setText("Show Consensus Logo");
1061 showSequenceLogo.addActionListener(new ActionListener()
1064 public void actionPerformed(ActionEvent e)
1066 showSequenceLogo_actionPerformed(e);
1070 applyAutoAnnotationSettings.setText("Apply to all groups");
1071 applyAutoAnnotationSettings.setState(false);
1072 applyAutoAnnotationSettings.setVisible(true);
1073 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1076 public void actionPerformed(ActionEvent e)
1078 applyAutoAnnotationSettings_actionPerformed(e);
1083 nucleotideColour.setText("Nucleotide");
1084 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1086 public void actionPerformed(ActionEvent e)
1088 nucleotideColour_actionPerformed(e);
1091 deleteGroups.setText("Undefine groups");
1092 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1093 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1094 .getMenuShortcutKeyMask(), false));
1095 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1097 public void actionPerformed(ActionEvent e)
1099 deleteGroups_actionPerformed(e);
1102 copy.setText("Copy");
1103 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1104 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1105 .getMenuShortcutKeyMask(), false));
1107 copy.addActionListener(new java.awt.event.ActionListener()
1109 public void actionPerformed(ActionEvent e)
1111 copy_actionPerformed(e);
1115 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1116 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1117 .getMenuShortcutKeyMask(), false));
1118 cut.addActionListener(new java.awt.event.ActionListener()
1120 public void actionPerformed(ActionEvent e)
1122 cut_actionPerformed(e);
1125 delete.setText("Delete");
1126 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1127 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1128 delete.addActionListener(new java.awt.event.ActionListener()
1130 public void actionPerformed(ActionEvent e)
1132 delete_actionPerformed(e);
1135 pasteMenu.setText("Paste");
1136 pasteNew.setText("To New Alignment");
1137 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1138 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1139 .getMenuShortcutKeyMask()
1140 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1141 pasteNew.addActionListener(new java.awt.event.ActionListener()
1143 public void actionPerformed(ActionEvent e)
1145 pasteNew_actionPerformed(e);
1148 pasteThis.setText("Add To This Alignment");
1149 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1150 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1151 .getMenuShortcutKeyMask(), false));
1152 pasteThis.addActionListener(new java.awt.event.ActionListener()
1154 public void actionPerformed(ActionEvent e)
1156 pasteThis_actionPerformed(e);
1159 applyToAllGroups.setText("Apply Colour To All Groups");
1160 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1162 public void actionPerformed(ActionEvent e)
1164 applyToAllGroups_actionPerformed(e);
1167 createPNG.addActionListener(new java.awt.event.ActionListener()
1169 public void actionPerformed(ActionEvent e)
1174 createPNG.setActionCommand("Save As PNG Image");
1175 createPNG.setText("PNG");
1176 font.setText("Font...");
1177 font.addActionListener(new java.awt.event.ActionListener()
1179 public void actionPerformed(ActionEvent e)
1181 font_actionPerformed(e);
1185 seqLimits.setText("Show Sequence Limits");
1186 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1187 seqLimits.addActionListener(new java.awt.event.ActionListener()
1189 public void actionPerformed(ActionEvent e)
1191 seqLimit_actionPerformed(e);
1194 epsFile.setText("EPS");
1195 epsFile.addActionListener(new java.awt.event.ActionListener()
1197 public void actionPerformed(ActionEvent e)
1202 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1203 LoadtreeMenuItem.setText("Load Associated Tree");
1204 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1206 public void actionPerformed(ActionEvent e)
1208 LoadtreeMenuItem_actionPerformed(e);
1211 scaleAbove.setVisible(false);
1212 scaleAbove.setText("Scale Above");
1213 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1215 public void actionPerformed(ActionEvent e)
1217 scaleAbove_actionPerformed(e);
1220 scaleLeft.setVisible(false);
1221 scaleLeft.setSelected(true);
1222 scaleLeft.setText("Scale Left");
1223 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1225 public void actionPerformed(ActionEvent e)
1227 scaleLeft_actionPerformed(e);
1230 scaleRight.setVisible(false);
1231 scaleRight.setSelected(true);
1232 scaleRight.setText("Scale Right");
1233 scaleRight.addActionListener(new java.awt.event.ActionListener()
1235 public void actionPerformed(ActionEvent e)
1237 scaleRight_actionPerformed(e);
1240 centreColumnLabelsMenuItem.setVisible(true);
1241 centreColumnLabelsMenuItem.setState(false);
1242 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1243 centreColumnLabelsMenuItem
1244 .addActionListener(new java.awt.event.ActionListener()
1246 public void actionPerformed(ActionEvent e)
1248 centreColumnLabels_actionPerformed(e);
1251 followHighlightMenuItem.setVisible(true);
1252 followHighlightMenuItem.setState(true);
1253 followHighlightMenuItem.setText("Automatic Scrolling");
1254 followHighlightMenuItem.addActionListener(new ActionListener()
1257 public void actionPerformed(ActionEvent e)
1259 followHighlight_actionPerformed();
1264 modifyPID.setText("Modify Identity Threshold...");
1265 modifyPID.addActionListener(new java.awt.event.ActionListener()
1267 public void actionPerformed(ActionEvent e)
1269 modifyPID_actionPerformed(e);
1272 modifyConservation.setText("Modify Conservation Threshold...");
1274 .addActionListener(new java.awt.event.ActionListener()
1276 public void actionPerformed(ActionEvent e)
1278 modifyConservation_actionPerformed(e);
1281 sortByTreeMenu.setText("By Tree Order");
1282 sort.setText("Sort");
1283 sort.addMenuListener(new MenuListener()
1285 public void menuSelected(MenuEvent e)
1290 public void menuDeselected(MenuEvent e)
1294 public void menuCanceled(MenuEvent e)
1298 sortByAnnotScore.setText("by Score");
1299 sort.add(sortByAnnotScore);
1300 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1303 public void menuCanceled(MenuEvent e)
1307 public void menuDeselected(MenuEvent e)
1311 public void menuSelected(MenuEvent e)
1313 buildSortByAnnotationScoresMenu();
1316 sortByAnnotScore.setVisible(false);
1318 calculateTree.setText("Calculate Tree");
1320 jMenu2.setText("Export Image");
1321 padGapsMenuitem.setText("Pad Gaps");
1322 padGapsMenuitem.setState(jalview.bin.Cache
1323 .getDefault("PAD_GAPS", false));
1324 padGapsMenuitem.addActionListener(new ActionListener()
1326 public void actionPerformed(ActionEvent e)
1328 padGapsMenuitem_actionPerformed(e);
1331 vamsasStore.setVisible(false);
1332 vamsasStore.setText("VAMSAS store");
1333 vamsasStore.addActionListener(new ActionListener()
1335 public void actionPerformed(ActionEvent e)
1337 vamsasStore_actionPerformed(e);
1340 showTranslation.setText("Translate cDNA");
1341 showTranslation.addActionListener(new ActionListener()
1343 public void actionPerformed(ActionEvent e)
1345 showTranslation_actionPerformed(e);
1348 extractScores.setText("Extract Scores...");
1349 extractScores.addActionListener(new ActionListener()
1351 public void actionPerformed(ActionEvent e)
1353 extractScores_actionPerformed(e);
1356 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1358 showProducts.setText("Get Cross References");
1360 * showProducts.addActionListener(new ActionListener() {
1362 * public void actionPerformed(ActionEvent e) {
1363 * showProducts_actionPerformed(e); } });
1365 featureSettings.setText("Feature Settings...");
1366 featureSettings.addActionListener(new ActionListener()
1368 public void actionPerformed(ActionEvent e)
1370 featureSettings_actionPerformed(e);
1373 fetchSequence.setText("Fetch Sequence(s)...");
1374 fetchSequence.addActionListener(new ActionListener()
1376 public void actionPerformed(ActionEvent e)
1378 fetchSequence_actionPerformed(e);
1382 annotationColour.setText("By Annotation...");
1383 annotationColour.addActionListener(new ActionListener()
1385 public void actionPerformed(ActionEvent e)
1387 annotationColour_actionPerformed(e);
1390 associatedData.setText("Load Features / Annotations");
1391 associatedData.addActionListener(new ActionListener()
1393 public void actionPerformed(ActionEvent e)
1395 associatedData_actionPerformed(e);
1398 autoCalculate.setText("Autocalculate Consensus");
1399 autoCalculate.setState(jalview.bin.Cache.getDefault(
1400 "AUTO_CALC_CONSENSUS", true));
1401 autoCalculate.addActionListener(new ActionListener()
1403 public void actionPerformed(ActionEvent e)
1405 autoCalculate_actionPerformed(e);
1408 sortByTree.setText("Sort Alignment With New Tree");
1409 sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1410 sortByTree.setState(jalview.bin.Cache.getDefault(
1411 "SORT_BY_TREE", false));
1412 sortByTree.addActionListener(new ActionListener()
1414 public void actionPerformed(ActionEvent e)
1416 sortByTreeOption_actionPerformed(e);
1420 addSequenceMenu.setText("Add Sequences");
1421 addFromFile.setText("From File");
1422 addFromFile.addActionListener(new ActionListener()
1424 public void actionPerformed(ActionEvent e)
1426 addFromFile_actionPerformed(e);
1429 addFromText.setText("From Textbox");
1430 addFromText.addActionListener(new ActionListener()
1432 public void actionPerformed(ActionEvent e)
1434 addFromText_actionPerformed(e);
1437 addFromURL.setText("From URL");
1438 addFromURL.addActionListener(new ActionListener()
1440 public void actionPerformed(ActionEvent e)
1442 addFromURL_actionPerformed(e);
1445 exportFeatures.setText("Export Features...");
1446 exportFeatures.addActionListener(new ActionListener()
1448 public void actionPerformed(ActionEvent e)
1450 exportFeatures_actionPerformed(e);
1453 exportAnnotations.setText("Export Annotations...");
1454 exportAnnotations.addActionListener(new ActionListener()
1456 public void actionPerformed(ActionEvent e)
1458 exportAnnotations_actionPerformed(e);
1461 statusPanel.setLayout(gridLayout1);
1462 jMenu3.setText("Show");
1463 showAllSeqs.setText("All Sequences");
1464 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1465 showAllSeqs.addActionListener(new ActionListener()
1467 public void actionPerformed(ActionEvent e)
1469 showAllSeqs_actionPerformed(e);
1472 showAllColumns.setText("All Columns");
1473 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1474 showAllColumns.addActionListener(new ActionListener()
1476 public void actionPerformed(ActionEvent e)
1478 showAllColumns_actionPerformed(e);
1481 hideMenu.setText("Hide");
1482 hideSelSequences.setText("Selected Sequences");
1483 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1484 hideSelSequences.addActionListener(new ActionListener()
1486 public void actionPerformed(ActionEvent e)
1488 hideSelSequences_actionPerformed(e);
1491 hideSelColumns.setText("Selected Columns");
1492 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1493 hideSelColumns.addActionListener(new ActionListener()
1495 public void actionPerformed(ActionEvent e)
1497 hideSelColumns_actionPerformed(e);
1500 hideAllSelection.setText("Selected Region");
1501 hideAllSelection.addActionListener(new ActionListener()
1503 public void actionPerformed(ActionEvent e)
1505 hideAllSelection_actionPerformed(e);
1508 // TODO: should be hidden if no selection exists.
1509 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1510 hideAllButSelection.addActionListener(new ActionListener()
1512 public void actionPerformed(ActionEvent e)
1514 hideAllButSelection_actionPerformed(e);
1517 showAllhidden.setText("All Sequences and Columns");
1519 .setToolTipText("H toggles visibility of hidden or selected regions.");
1520 showAllhidden.addActionListener(new ActionListener()
1522 public void actionPerformed(ActionEvent e)
1524 showAllhidden_actionPerformed(e);
1528 hiddenMarkers.setText("Show Hidden Markers");
1529 hiddenMarkers.addActionListener(new ActionListener()
1531 public void actionPerformed(ActionEvent e)
1533 hiddenMarkers_actionPerformed(e);
1536 invertColSel.setText("Invert Column Selection");
1537 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1538 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1539 .getMenuShortcutKeyMask()
1540 | java.awt.event.KeyEvent.ALT_MASK, false));
1541 invertColSel.addActionListener(new ActionListener()
1543 public void actionPerformed(ActionEvent e)
1545 invertColSel_actionPerformed(e);
1548 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1550 public void stateChanged(ChangeEvent evt)
1552 JTabbedPane pane = (JTabbedPane) evt.getSource();
1553 int sel = pane.getSelectedIndex();
1554 tabSelectionChanged(sel);
1557 tabbedPane.addMouseListener(new MouseAdapter()
1559 public void mousePressed(MouseEvent e)
1561 tabbedPane_mousePressed(e);
1564 tabbedPane.addFocusListener(new FocusAdapter()
1566 public void focusGained(FocusEvent e)
1568 tabbedPane_focusGained(e);
1571 save.setText("Save");
1572 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1573 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1574 .getMenuShortcutKeyMask(), false));
1575 save.addActionListener(new ActionListener()
1577 public void actionPerformed(ActionEvent e)
1579 save_actionPerformed(e);
1582 reload.setEnabled(false);
1583 reload.setText("Reload");
1584 reload.addActionListener(new ActionListener()
1586 public void actionPerformed(ActionEvent e)
1588 reload_actionPerformed(e);
1591 newView.setText("New View");
1592 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1593 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1594 .getMenuShortcutKeyMask(), false));
1595 newView.addActionListener(new ActionListener()
1597 public void actionPerformed(ActionEvent e)
1599 newView_actionPerformed(e);
1602 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1603 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1604 textColour.setText("Colour Text ...");
1605 textColour.addActionListener(new ActionListener()
1607 public void actionPerformed(ActionEvent e)
1609 textColour_actionPerformed(e);
1612 formatMenu.setText("Format");
1613 selectMenu.setText("Select");
1614 idRightAlign.setText("Right Align Sequence Id");
1615 idRightAlign.addActionListener(new ActionListener()
1617 public void actionPerformed(ActionEvent e)
1619 idRightAlign_actionPerformed(e);
1622 gatherViews.setEnabled(false);
1623 gatherViews.setText("Gather Views");
1624 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1625 java.awt.event.KeyEvent.VK_G, 0, false));
1626 gatherViews.addActionListener(new ActionListener()
1628 public void actionPerformed(ActionEvent e)
1630 gatherViews_actionPerformed(e);
1633 expandViews.setEnabled(false);
1634 expandViews.setText("Expand Views");
1635 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1636 java.awt.event.KeyEvent.VK_X, 0, false));
1637 expandViews.addActionListener(new ActionListener()
1639 public void actionPerformed(ActionEvent e)
1641 expandViews_actionPerformed(e);
1644 pageSetup.setText("Page Setup ...");
1645 pageSetup.addActionListener(new ActionListener()
1647 public void actionPerformed(ActionEvent e)
1649 pageSetup_actionPerformed(e);
1652 alignmentProperties.setText("Alignment Properties...");
1653 alignmentProperties.addActionListener(new ActionListener()
1655 public void actionPerformed(ActionEvent actionEvent)
1657 alignmentProperties();
1660 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1661 autoAnnMenu.setText("Autocalculated Annotation");
1662 alignFrameMenuBar.add(fileMenu);
1663 alignFrameMenuBar.add(editMenu);
1664 alignFrameMenuBar.add(selectMenu);
1665 alignFrameMenuBar.add(viewMenu);
1666 alignFrameMenuBar.add(formatMenu);
1667 alignFrameMenuBar.add(colourMenu);
1668 alignFrameMenuBar.add(calculateMenu);
1669 alignFrameMenuBar.add(webService);
1670 fileMenu.add(fetchSequence);
1671 fileMenu.add(addSequenceMenu);
1672 fileMenu.add(reload);
1673 fileMenu.addSeparator();
1674 fileMenu.add(vamsasStore);
1676 fileMenu.add(saveAs);
1677 fileMenu.add(outputTextboxMenu);
1678 fileMenu.add(pageSetup);
1679 fileMenu.add(printMenuItem);
1680 fileMenu.addSeparator();
1681 fileMenu.add(jMenu2);
1682 fileMenu.add(exportFeatures);
1683 fileMenu.add(exportAnnotations);
1684 fileMenu.add(LoadtreeMenuItem);
1685 fileMenu.add(associatedData);
1686 fileMenu.addSeparator();
1687 fileMenu.add(closeMenuItem);
1688 editMenu.add(undoMenuItem);
1689 editMenu.add(redoMenuItem);
1692 editMenu.add(pasteMenu);
1693 editMenu.add(delete);
1694 editMenu.addSeparator();
1695 editMenu.add(remove2LeftMenuItem);
1696 editMenu.add(remove2RightMenuItem);
1697 editMenu.add(removeGappedColumnMenuItem);
1698 editMenu.add(removeAllGapsMenuItem);
1699 editMenu.add(removeRedundancyMenuItem);
1700 editMenu.addSeparator();
1701 // dont add these yet in the CVS build - they cannot be undone!
1702 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1703 // editMenu.add(justifyLeftMenuItem);
1704 // editMenu.add(justifyRightMenuItem);
1705 // editMenu.addSeparator();
1706 editMenu.add(padGapsMenuitem);
1707 viewMenu.add(newView);
1708 viewMenu.add(expandViews);
1709 viewMenu.add(gatherViews);
1710 viewMenu.addSeparator();
1711 viewMenu.add(jMenu3);
1712 viewMenu.add(hideMenu);
1713 viewMenu.addSeparator();
1714 viewMenu.add(followHighlightMenuItem);
1715 viewMenu.add(annotationPanelMenuItem);
1716 autoAnnMenu.add(applyAutoAnnotationSettings);
1717 autoAnnMenu.add(showConsensusHistogram);
1718 autoAnnMenu.add(showSequenceLogo);
1719 autoAnnMenu.addSeparator();
1720 autoAnnMenu.add(showGroupConservation);
1721 autoAnnMenu.add(showGroupConsensus);
1722 viewMenu.add(autoAnnMenu);
1723 viewMenu.addSeparator();
1724 viewMenu.add(showSeqFeatures);
1725 // viewMenu.add(showSeqFeaturesHeight);
1727 viewMenu.add(featureSettings);
1728 tooltipSettingsMenu.add(showDbRefsMenuitem);
1729 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1730 viewMenu.add(tooltipSettingsMenu);
1731 viewMenu.addSeparator();
1732 viewMenu.add(alignmentProperties);
1733 viewMenu.addSeparator();
1734 viewMenu.add(overviewMenuItem);
1735 colourMenu.add(applyToAllGroups);
1736 colourMenu.add(textColour);
1737 colourMenu.addSeparator();
1738 colourMenu.add(noColourmenuItem);
1739 colourMenu.add(clustalColour);
1740 colourMenu.add(BLOSUM62Colour);
1741 colourMenu.add(PIDColour);
1742 colourMenu.add(zappoColour);
1743 colourMenu.add(taylorColour);
1744 colourMenu.add(hydrophobicityColour);
1745 colourMenu.add(helixColour);
1746 colourMenu.add(strandColour);
1747 colourMenu.add(turnColour);
1748 colourMenu.add(buriedColour);
1749 colourMenu.add(nucleotideColour);
1750 colourMenu.add(userDefinedColour);
1751 colourMenu.addSeparator();
1752 colourMenu.add(conservationMenuItem);
1753 colourMenu.add(modifyConservation);
1754 colourMenu.add(abovePIDThreshold);
1755 colourMenu.add(modifyPID);
1756 colourMenu.add(annotationColour);
1757 calculateMenu.add(sort);
1758 calculateMenu.add(calculateTree);
1759 calculateMenu.addSeparator();
1760 calculateMenu.add(pairwiseAlignmentMenuItem);
1761 calculateMenu.add(PCAMenuItem);
1762 calculateMenu.addSeparator();
1763 calculateMenu.add(showTranslation);
1764 calculateMenu.add(showProducts);
1765 calculateMenu.add(autoCalculate);
1766 calculateMenu.add(sortByTree);
1767 calculateMenu.addSeparator();
1768 calculateMenu.add(extractScores);
1769 webServiceNoServices = new JMenuItem("<No Services>");
1770 webService.add(webServiceNoServices);
1771 pasteMenu.add(pasteNew);
1772 pasteMenu.add(pasteThis);
1773 sort.add(sortIDMenuItem);
1774 sort.add(sortLengthMenuItem);
1775 sort.add(sortGroupMenuItem);
1776 sort.add(sortPairwiseMenuItem);
1777 sort.add(sortByTreeMenu);
1778 calculateTree.add(averageDistanceTreeMenuItem);
1779 calculateTree.add(neighbourTreeMenuItem);
1780 calculateTree.add(avDistanceTreeBlosumMenuItem);
1781 calculateTree.add(njTreeBlosumMenuItem);
1782 jMenu2.add(htmlMenuItem);
1783 jMenu2.add(epsFile);
1784 jMenu2.add(createPNG);
1785 addSequenceMenu.add(addFromFile);
1786 addSequenceMenu.add(addFromText);
1787 addSequenceMenu.add(addFromURL);
1788 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1789 statusPanel.add(statusBar, null);
1790 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1791 jMenu3.add(showAllColumns);
1792 jMenu3.add(showAllSeqs);
1793 jMenu3.add(showAllhidden);
1794 hideMenu.add(hideSelColumns);
1795 hideMenu.add(hideSelSequences);
1796 hideMenu.add(hideAllSelection);
1797 hideMenu.add(hideAllButSelection);
1799 formatMenu.add(font);
1800 formatMenu.addSeparator();
1801 formatMenu.add(wrapMenuItem);
1802 formatMenu.add(scaleAbove);
1803 formatMenu.add(scaleLeft);
1804 formatMenu.add(scaleRight);
1805 formatMenu.add(seqLimits);
1806 formatMenu.add(idRightAlign);
1807 formatMenu.add(hiddenMarkers);
1808 formatMenu.add(viewBoxesMenuItem);
1809 formatMenu.add(viewTextMenuItem);
1810 formatMenu.add(colourTextMenuItem);
1811 formatMenu.add(renderGapsMenuItem);
1812 formatMenu.add(centreColumnLabelsMenuItem);
1813 formatMenu.add(showNonconservedMenuItem);
1814 selectMenu.add(findMenuItem);
1815 selectMenu.addSeparator();
1816 selectMenu.add(selectAllSequenceMenuItem);
1817 selectMenu.add(deselectAllSequenceMenuItem);
1818 selectMenu.add(invertSequenceMenuItem);
1819 selectMenu.add(invertColSel);
1820 selectMenu.add(deleteGroups);
1821 selectMenu.add(grpsFromSelection);
1824 protected void showAllhidden_actionPerformed(ActionEvent e)
1826 // TODO Auto-generated method stub
1830 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1832 // TODO Auto-generated method stub
1836 protected void hideAllSelection_actionPerformed(ActionEvent e)
1838 // TODO Auto-generated method stub
1842 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1844 // TODO Auto-generated method stub
1848 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1850 // TODO Auto-generated method stub
1854 protected void showSequenceLogo_actionPerformed(ActionEvent e)
1856 // TODO Auto-generated method stub
1860 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1862 // TODO Auto-generated method stub
1866 protected void showGroupConsensus_actionPerformed(ActionEvent e)
1868 // TODO Auto-generated method stub
1872 protected void showGroupConservation_actionPerformed(ActionEvent e)
1874 // TODO Auto-generated method stub
1878 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1880 // TODO Auto-generated method stub
1884 protected void showSeqFeaturesHeight_actionPerformed(
1885 ActionEvent actionEvent)
1887 // TODO Auto-generated method stub
1891 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1893 // TODO Auto-generated method stub
1897 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1899 // TODO Auto-generated method stub
1903 protected void followHighlight_actionPerformed()
1905 // TODO Auto-generated method stub
1909 protected void showNpFeats_actionPerformed(ActionEvent e)
1911 // TODO Auto-generated method stub
1915 protected void showDbRefs_actionPerformed(ActionEvent e)
1917 // TODO Auto-generated method stub
1921 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1925 protected void showProducts_actionPerformed(ActionEvent e)
1929 protected void buildSortByAnnotationScoresMenu()
1933 protected void extractScores_actionPerformed(ActionEvent e)
1937 protected void outputText_actionPerformed(ActionEvent e)
1941 public void addFromFile_actionPerformed(ActionEvent e)
1946 public void addFromText_actionPerformed(ActionEvent e)
1951 public void addFromURL_actionPerformed(ActionEvent e)
1956 public void exportFeatures_actionPerformed(ActionEvent e)
1961 public void exportAnnotations_actionPerformed(ActionEvent e)
1966 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1970 protected void closeMenuItem_actionPerformed(boolean b)
1974 protected void redoMenuItem_actionPerformed(ActionEvent e)
1978 protected void undoMenuItem_actionPerformed(ActionEvent e)
1982 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1986 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1990 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1994 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1998 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2002 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2006 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2010 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2014 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2018 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2022 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2026 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2030 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2034 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2038 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2042 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2046 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2050 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2054 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2058 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2062 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2066 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2070 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2074 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2078 protected void clustalColour_actionPerformed(ActionEvent e)
2082 protected void zappoColour_actionPerformed(ActionEvent e)
2086 protected void taylorColour_actionPerformed(ActionEvent e)
2090 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2094 protected void helixColour_actionPerformed(ActionEvent e)
2098 protected void strandColour_actionPerformed(ActionEvent e)
2102 protected void turnColour_actionPerformed(ActionEvent e)
2106 protected void buriedColour_actionPerformed(ActionEvent e)
2110 protected void userDefinedColour_actionPerformed(ActionEvent e)
2114 protected void PIDColour_actionPerformed(ActionEvent e)
2118 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2122 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2126 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2130 protected void printMenuItem_actionPerformed(ActionEvent e)
2134 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2138 protected void findMenuItem_actionPerformed(ActionEvent e)
2142 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2146 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2150 protected void nucleotideColour_actionPerformed(ActionEvent e)
2154 protected void deleteGroups_actionPerformed(ActionEvent e)
2158 protected void copy_actionPerformed(ActionEvent e)
2162 protected void cut_actionPerformed(ActionEvent e)
2166 protected void delete_actionPerformed(ActionEvent e)
2170 protected void pasteNew_actionPerformed(ActionEvent e)
2174 protected void pasteThis_actionPerformed(ActionEvent e)
2178 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2182 public void createPNG(java.io.File f)
2186 protected void font_actionPerformed(ActionEvent e)
2190 protected void seqLimit_actionPerformed(ActionEvent e)
2194 public void seqDBRef_actionPerformed(ActionEvent e)
2199 public void createEPS(java.io.File f)
2203 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2207 protected void jpred_actionPerformed(ActionEvent e)
2211 protected void scaleAbove_actionPerformed(ActionEvent e)
2215 protected void scaleLeft_actionPerformed(ActionEvent e)
2219 protected void scaleRight_actionPerformed(ActionEvent e)
2223 protected void modifyPID_actionPerformed(ActionEvent e)
2227 protected void modifyConservation_actionPerformed(ActionEvent e)
2231 protected void saveAs_actionPerformed(ActionEvent e)
2235 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2239 public void vamsasStore_actionPerformed(ActionEvent e)
2244 public void vamsasLoad_actionPerformed(ActionEvent e)
2249 public void showTranslation_actionPerformed(ActionEvent e)
2254 public void featureSettings_actionPerformed(ActionEvent e)
2259 public void fetchSequence_actionPerformed(ActionEvent e)
2264 public void smoothFont_actionPerformed(ActionEvent e)
2269 public void annotationColour_actionPerformed(ActionEvent e)
2274 public void associatedData_actionPerformed(ActionEvent e)
2279 public void autoCalculate_actionPerformed(ActionEvent e)
2284 public void sortByTreeOption_actionPerformed(ActionEvent e)
2289 public void showAllSeqs_actionPerformed(ActionEvent e)
2294 public void showAllColumns_actionPerformed(ActionEvent e)
2299 public void hideSelSequences_actionPerformed(ActionEvent e)
2304 public void hideSelColumns_actionPerformed(ActionEvent e)
2309 public void hiddenMarkers_actionPerformed(ActionEvent e)
2314 public void findPdbId_actionPerformed(ActionEvent e)
2319 public void enterPdbId_actionPerformed(ActionEvent e)
2324 public void pdbFile_actionPerformed(ActionEvent e)
2329 public void invertColSel_actionPerformed(ActionEvent e)
2334 public void tabSelectionChanged(int sel)
2339 public void tabbedPane_mousePressed(MouseEvent e)
2344 public void tabbedPane_focusGained(FocusEvent e)
2349 public void save_actionPerformed(ActionEvent e)
2354 public void reload_actionPerformed(ActionEvent e)
2359 public void newView_actionPerformed(ActionEvent e)
2364 public void textColour_actionPerformed(ActionEvent e)
2369 public void idRightAlign_actionPerformed(ActionEvent e)
2374 public void expandViews_actionPerformed(ActionEvent e)
2379 public void gatherViews_actionPerformed(ActionEvent e)
2384 public void buildTreeMenu()
2389 public void pageSetup_actionPerformed(ActionEvent e)
2394 public void alignmentProperties()