2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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 JMenu addSequenceMenu = new JMenu();
226 JMenuItem addFromFile = new JMenuItem();
228 JMenuItem addFromText = new JMenuItem();
230 JMenuItem addFromURL = new JMenuItem();
232 JMenuItem exportAnnotations = new JMenuItem();
234 JMenuItem exportFeatures = new JMenuItem();
236 protected JPanel statusPanel = new JPanel();
238 GridLayout gridLayout1 = new GridLayout();
240 JMenu jMenu3 = new JMenu();
242 JMenuItem showAllSeqs = new JMenuItem();
244 JMenuItem showAllColumns = new JMenuItem();
246 JMenu hideMenu = new JMenu();
248 JMenuItem hideSelSequences = new JMenuItem();
250 JMenuItem hideSelColumns = new JMenuItem();
252 JMenuItem hideAllButSelection = new JMenuItem();
254 JMenuItem hideAllSelection = new JMenuItem();
256 JMenuItem showAllhidden = new JMenuItem();
258 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
260 JMenuItem invertColSel = new JMenuItem();
262 protected JTabbedPane tabbedPane = new JTabbedPane();
264 JMenuItem save = new JMenuItem();
266 protected JMenuItem reload = new JMenuItem();
268 JMenuItem newView = new JMenuItem();
270 JMenuItem textColour = new JMenuItem();
272 JMenu formatMenu = new JMenu();
274 JMenu selectMenu = new JMenu();
276 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
278 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
280 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
282 protected JMenuItem gatherViews = new JMenuItem();
284 protected JMenuItem expandViews = new JMenuItem();
286 JMenuItem pageSetup = new JMenuItem();
288 JMenuItem alignmentProperties = new JMenuItem();
290 JMenu tooltipSettingsMenu = new JMenu();
292 private JMenuItem justifyLeftMenuItem = new JMenuItem();
294 private JMenuItem justifyRightMenuItem = new JMenuItem();
296 JMenu autoAnnMenu = new JMenu();
298 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
300 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
302 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
304 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
306 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
308 private JMenuItem grpsFromSelection = new JMenuItem();
315 setJMenuBar(alignFrameMenuBar);
317 // dynamically fill save as menu with available formats
318 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
320 JMenuItem item = new JMenuItem(
321 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
323 item.addActionListener(new java.awt.event.ActionListener()
325 public void actionPerformed(ActionEvent e)
327 outputText_actionPerformed(e);
331 outputTextboxMenu.add(item);
333 } catch (Exception e)
337 if (!new jalview.util.Platform().isAMac())
339 closeMenuItem.setMnemonic('C');
340 outputTextboxMenu.setMnemonic('T');
341 undoMenuItem.setMnemonic('Z');
342 redoMenuItem.setMnemonic('0');
343 copy.setMnemonic('C');
344 cut.setMnemonic('U');
345 pasteMenu.setMnemonic('P');
346 reload.setMnemonic('R');
349 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
351 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
352 .getUserColourSchemes().keys();
354 while (userColours.hasMoreElements())
356 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
357 userColours.nextElement().toString());
358 radioItem.setName("USER_DEFINED");
359 radioItem.addMouseListener(new MouseAdapter()
361 public void mousePressed(MouseEvent evt)
363 if (evt.isControlDown()
364 || SwingUtilities.isRightMouseButton(evt))
367 .removeActionListener(radioItem.getActionListeners()[0]);
369 int option = JOptionPane.showInternalConfirmDialog(
370 jalview.gui.Desktop.desktop,
371 "Remove from default list?",
372 "Remove user defined colour",
373 JOptionPane.YES_NO_OPTION);
374 if (option == JOptionPane.YES_OPTION)
376 jalview.gui.UserDefinedColours
377 .removeColourFromDefaults(radioItem.getText());
378 colourMenu.remove(radioItem);
382 radioItem.addActionListener(new ActionListener()
384 public void actionPerformed(ActionEvent evt)
386 userDefinedColour_actionPerformed(evt);
393 radioItem.addActionListener(new ActionListener()
395 public void actionPerformed(ActionEvent evt)
397 userDefinedColour_actionPerformed(evt);
400 colourMenu.insert(radioItem, 15);
401 colours.add(radioItem);
404 colours.add(noColourmenuItem);
405 colours.add(clustalColour);
406 colours.add(zappoColour);
407 colours.add(taylorColour);
408 colours.add(hydrophobicityColour);
409 colours.add(helixColour);
410 colours.add(strandColour);
411 colours.add(turnColour);
412 colours.add(buriedColour);
413 colours.add(userDefinedColour);
414 colours.add(PIDColour);
415 colours.add(BLOSUM62Colour);
416 colours.add(nucleotideColour);
418 setColourSelected(jalview.bin.Cache
419 .getDefault("DEFAULT_COLOUR", "None"));
423 public void setColourSelected(String defaultColour)
426 if (defaultColour != null)
428 int index = ColourSchemeProperty
429 .getColourIndexFromName(defaultColour);
433 case ColourSchemeProperty.NONE:
434 noColourmenuItem.setSelected(true);
436 case ColourSchemeProperty.CLUSTAL:
437 clustalColour.setSelected(true);
441 case ColourSchemeProperty.BLOSUM:
442 BLOSUM62Colour.setSelected(true);
446 case ColourSchemeProperty.PID:
447 PIDColour.setSelected(true);
451 case ColourSchemeProperty.ZAPPO:
452 zappoColour.setSelected(true);
456 case ColourSchemeProperty.TAYLOR:
457 taylorColour.setSelected(true);
460 case ColourSchemeProperty.HYDROPHOBIC:
461 hydrophobicityColour.setSelected(true);
465 case ColourSchemeProperty.HELIX:
466 helixColour.setSelected(true);
470 case ColourSchemeProperty.STRAND:
471 strandColour.setSelected(true);
475 case ColourSchemeProperty.TURN:
476 turnColour.setSelected(true);
480 case ColourSchemeProperty.BURIED:
481 buriedColour.setSelected(true);
485 case ColourSchemeProperty.NUCLEOTIDE:
486 nucleotideColour.setSelected(true);
490 case ColourSchemeProperty.USER_DEFINED:
491 userDefinedColour.setSelected(true);
499 private void jbInit() throws Exception
501 fileMenu.setText("File");
502 saveAs.setText("Save As...");
503 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
504 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
505 .getMenuShortcutKeyMask()
506 | java.awt.event.KeyEvent.SHIFT_MASK, false));
507 saveAs.addActionListener(new ActionListener()
509 public void actionPerformed(ActionEvent e)
511 saveAs_actionPerformed(e);
514 closeMenuItem.setText("Close");
515 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
516 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
517 .getMenuShortcutKeyMask(), false));
518 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
520 public void actionPerformed(ActionEvent e)
522 closeMenuItem_actionPerformed(false);
525 editMenu.setText("Edit");
526 viewMenu.setText("View");
527 colourMenu.setText("Colour");
528 calculateMenu.setText("Calculate");
529 webService.setText("Web Service");
530 selectAllSequenceMenuItem.setText("Select All");
531 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
532 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
533 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
534 selectAllSequenceMenuItem
535 .addActionListener(new java.awt.event.ActionListener()
537 public void actionPerformed(ActionEvent e)
539 selectAllSequenceMenuItem_actionPerformed(e);
542 deselectAllSequenceMenuItem.setText("Deselect All");
543 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
544 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
545 deselectAllSequenceMenuItem
546 .addActionListener(new java.awt.event.ActionListener()
548 public void actionPerformed(ActionEvent e)
550 deselectAllSequenceMenuItem_actionPerformed(e);
553 invertSequenceMenuItem.setText("Invert Sequence Selection");
554 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
555 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
556 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
557 invertSequenceMenuItem
558 .addActionListener(new java.awt.event.ActionListener()
560 public void actionPerformed(ActionEvent e)
562 invertSequenceMenuItem_actionPerformed(e);
565 grpsFromSelection.setText("Make Groups for selection");
566 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
568 public void actionPerformed(ActionEvent e)
570 makeGrpsFromSelection_actionPerformed(e);
574 remove2LeftMenuItem.setText("Remove Left");
575 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
576 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
577 .getMenuShortcutKeyMask(), false));
579 .addActionListener(new java.awt.event.ActionListener()
581 public void actionPerformed(ActionEvent e)
583 remove2LeftMenuItem_actionPerformed(e);
586 remove2RightMenuItem.setText("Remove Right");
587 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
588 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
589 .getMenuShortcutKeyMask(), false));
591 .addActionListener(new java.awt.event.ActionListener()
593 public void actionPerformed(ActionEvent e)
595 remove2RightMenuItem_actionPerformed(e);
598 removeGappedColumnMenuItem.setText("Remove Empty Columns");
599 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
600 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
601 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
602 removeGappedColumnMenuItem
603 .addActionListener(new java.awt.event.ActionListener()
605 public void actionPerformed(ActionEvent e)
607 removeGappedColumnMenuItem_actionPerformed(e);
610 removeAllGapsMenuItem.setText("Remove All Gaps");
611 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
612 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
613 .getDefaultToolkit().getMenuShortcutKeyMask()
614 | java.awt.event.KeyEvent.SHIFT_MASK, false));
615 removeAllGapsMenuItem
616 .addActionListener(new java.awt.event.ActionListener()
618 public void actionPerformed(ActionEvent e)
620 removeAllGapsMenuItem_actionPerformed(e);
623 justifyLeftMenuItem.setText("Left Justify Alignment");
625 .addActionListener(new java.awt.event.ActionListener()
627 public void actionPerformed(ActionEvent e)
629 justifyLeftMenuItem_actionPerformed(e);
632 justifyRightMenuItem.setText("Right Justify Alignment");
634 .addActionListener(new java.awt.event.ActionListener()
636 public void actionPerformed(ActionEvent e)
638 justifyRightMenuItem_actionPerformed(e);
641 viewBoxesMenuItem.setText("Boxes");
642 viewBoxesMenuItem.setState(true);
643 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
645 public void actionPerformed(ActionEvent e)
647 viewBoxesMenuItem_actionPerformed(e);
650 viewTextMenuItem.setText("Text");
651 viewTextMenuItem.setState(true);
652 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
654 public void actionPerformed(ActionEvent e)
656 viewTextMenuItem_actionPerformed(e);
659 showNonconservedMenuItem.setText("Show nonconserved");
660 showNonconservedMenuItem.setState(false);
661 showNonconservedMenuItem
662 .addActionListener(new java.awt.event.ActionListener()
664 public void actionPerformed(ActionEvent e)
666 showUnconservedMenuItem_actionPerformed(e);
669 sortPairwiseMenuItem.setText("by Pairwise Identity");
671 .addActionListener(new java.awt.event.ActionListener()
673 public void actionPerformed(ActionEvent e)
675 sortPairwiseMenuItem_actionPerformed(e);
678 sortIDMenuItem.setText("by ID");
679 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
681 public void actionPerformed(ActionEvent e)
683 sortIDMenuItem_actionPerformed(e);
686 sortLengthMenuItem.setText("By Length");
688 .addActionListener(new java.awt.event.ActionListener()
690 public void actionPerformed(ActionEvent e)
692 sortLengthMenuItem_actionPerformed(e);
695 sortGroupMenuItem.setText("by Group");
696 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
698 public void actionPerformed(ActionEvent e)
700 sortGroupMenuItem_actionPerformed(e);
703 removeRedundancyMenuItem.setText("Remove Redundancy...");
704 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
705 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
706 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
707 removeRedundancyMenuItem
708 .addActionListener(new java.awt.event.ActionListener()
710 public void actionPerformed(ActionEvent e)
712 removeRedundancyMenuItem_actionPerformed(e);
715 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
716 pairwiseAlignmentMenuItem
717 .addActionListener(new java.awt.event.ActionListener()
719 public void actionPerformed(ActionEvent e)
721 pairwiseAlignmentMenuItem_actionPerformed(e);
724 PCAMenuItem.setText("Principal Component Analysis");
725 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
727 public void actionPerformed(ActionEvent e)
729 PCAMenuItem_actionPerformed(e);
732 averageDistanceTreeMenuItem
733 .setText("Average Distance Using % Identity");
734 averageDistanceTreeMenuItem
735 .addActionListener(new java.awt.event.ActionListener()
737 public void actionPerformed(ActionEvent e)
739 averageDistanceTreeMenuItem_actionPerformed(e);
742 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
743 neighbourTreeMenuItem
744 .addActionListener(new java.awt.event.ActionListener()
746 public void actionPerformed(ActionEvent e)
748 neighbourTreeMenuItem_actionPerformed(e);
751 this.getContentPane().setLayout(borderLayout1);
752 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
753 statusBar.setBackground(Color.white);
754 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
755 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
756 statusBar.setText("Status bar");
757 outputTextboxMenu.setText("Output to Textbox");
758 clustalColour.setText("Clustalx");
760 clustalColour.addActionListener(new java.awt.event.ActionListener()
762 public void actionPerformed(ActionEvent e)
764 clustalColour_actionPerformed(e);
767 zappoColour.setText("Zappo");
768 zappoColour.addActionListener(new java.awt.event.ActionListener()
770 public void actionPerformed(ActionEvent e)
772 zappoColour_actionPerformed(e);
775 taylorColour.setText("Taylor");
776 taylorColour.addActionListener(new java.awt.event.ActionListener()
778 public void actionPerformed(ActionEvent e)
780 taylorColour_actionPerformed(e);
783 hydrophobicityColour.setText("Hydrophobicity");
785 .addActionListener(new java.awt.event.ActionListener()
787 public void actionPerformed(ActionEvent e)
789 hydrophobicityColour_actionPerformed(e);
792 helixColour.setText("Helix Propensity");
793 helixColour.addActionListener(new java.awt.event.ActionListener()
795 public void actionPerformed(ActionEvent e)
797 helixColour_actionPerformed(e);
800 strandColour.setText("Strand Propensity");
801 strandColour.addActionListener(new java.awt.event.ActionListener()
803 public void actionPerformed(ActionEvent e)
805 strandColour_actionPerformed(e);
808 turnColour.setText("Turn Propensity");
809 turnColour.addActionListener(new java.awt.event.ActionListener()
811 public void actionPerformed(ActionEvent e)
813 turnColour_actionPerformed(e);
816 buriedColour.setText("Buried Index");
817 buriedColour.addActionListener(new java.awt.event.ActionListener()
819 public void actionPerformed(ActionEvent e)
821 buriedColour_actionPerformed(e);
824 userDefinedColour.setText("User Defined...");
825 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
827 public void actionPerformed(ActionEvent e)
829 userDefinedColour_actionPerformed(e);
832 PIDColour.setText("Percentage Identity");
833 PIDColour.addActionListener(new java.awt.event.ActionListener()
835 public void actionPerformed(ActionEvent e)
837 PIDColour_actionPerformed(e);
840 BLOSUM62Colour.setText("BLOSUM62 Score");
841 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
843 public void actionPerformed(ActionEvent e)
845 BLOSUM62Colour_actionPerformed(e);
848 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
849 avDistanceTreeBlosumMenuItem
850 .addActionListener(new java.awt.event.ActionListener()
852 public void actionPerformed(ActionEvent e)
854 avTreeBlosumMenuItem_actionPerformed(e);
857 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
859 .addActionListener(new java.awt.event.ActionListener()
861 public void actionPerformed(ActionEvent e)
863 njTreeBlosumMenuItem_actionPerformed(e);
866 annotationPanelMenuItem.setActionCommand("");
867 annotationPanelMenuItem.setText("Show Annotations");
868 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
869 "SHOW_ANNOTATIONS", true));
870 annotationPanelMenuItem
871 .addActionListener(new java.awt.event.ActionListener()
873 public void actionPerformed(ActionEvent e)
875 annotationPanelMenuItem_actionPerformed(e);
878 colourTextMenuItem.setText("Colour Text");
880 .addActionListener(new java.awt.event.ActionListener()
882 public void actionPerformed(ActionEvent e)
884 colourTextMenuItem_actionPerformed(e);
887 htmlMenuItem.setText("HTML");
888 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
890 public void actionPerformed(ActionEvent e)
892 htmlMenuItem_actionPerformed(e);
895 overviewMenuItem.setText("Overview Window");
896 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
898 public void actionPerformed(ActionEvent e)
900 overviewMenuItem_actionPerformed(e);
903 undoMenuItem.setEnabled(false);
904 undoMenuItem.setText("Undo");
905 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
906 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
907 .getMenuShortcutKeyMask(), false));
908 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
910 public void actionPerformed(ActionEvent e)
912 undoMenuItem_actionPerformed(e);
915 redoMenuItem.setEnabled(false);
916 redoMenuItem.setText("Redo");
917 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
918 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
919 .getMenuShortcutKeyMask(), false));
920 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
922 public void actionPerformed(ActionEvent e)
924 redoMenuItem_actionPerformed(e);
927 conservationMenuItem.setText("By Conservation");
929 .addActionListener(new java.awt.event.ActionListener()
931 public void actionPerformed(ActionEvent e)
933 conservationMenuItem_actionPerformed(e);
936 noColourmenuItem.setText("None");
937 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
939 public void actionPerformed(ActionEvent e)
941 noColourmenuItem_actionPerformed(e);
944 wrapMenuItem.setText("Wrap");
945 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
947 public void actionPerformed(ActionEvent e)
949 wrapMenuItem_actionPerformed(e);
952 printMenuItem.setText("Print ...");
953 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
954 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
955 .getMenuShortcutKeyMask(), false));
956 printMenuItem.addActionListener(new java.awt.event.ActionListener()
958 public void actionPerformed(ActionEvent e)
960 printMenuItem_actionPerformed(e);
963 renderGapsMenuItem.setText("Show Gaps");
964 renderGapsMenuItem.setState(true);
966 .addActionListener(new java.awt.event.ActionListener()
968 public void actionPerformed(ActionEvent e)
970 renderGapsMenuItem_actionPerformed(e);
973 findMenuItem.setText("Find...");
974 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
975 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
976 .getMenuShortcutKeyMask(), false));
977 findMenuItem.addActionListener(new java.awt.event.ActionListener()
979 public void actionPerformed(ActionEvent e)
981 findMenuItem_actionPerformed(e);
984 abovePIDThreshold.setText("Above Identity Threshold");
985 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
987 public void actionPerformed(ActionEvent e)
989 abovePIDThreshold_actionPerformed(e);
992 showSeqFeatures.setText("Show Sequence Features");
993 showSeqFeatures.addActionListener(new ActionListener()
995 public void actionPerformed(ActionEvent actionEvent)
997 showSeqFeatures_actionPerformed(actionEvent);
1001 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1002 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1003 * void actionPerformed(ActionEvent actionEvent) {
1004 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1006 showDbRefsMenuitem.setText("Show Database Refs");
1007 showDbRefsMenuitem.addActionListener(new ActionListener()
1010 public void actionPerformed(ActionEvent e)
1012 showDbRefs_actionPerformed(e);
1016 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1017 showNpFeatsMenuitem.addActionListener(new ActionListener()
1020 public void actionPerformed(ActionEvent e)
1022 showNpFeats_actionPerformed(e);
1026 showGroupConservation.setText("Group Conservation");
1027 showGroupConservation.addActionListener(new ActionListener()
1030 public void actionPerformed(ActionEvent e)
1032 showGroupConservation_actionPerformed(e);
1037 showGroupConsensus.setText("Group Consensus");
1038 showGroupConsensus.addActionListener(new ActionListener()
1041 public void actionPerformed(ActionEvent e)
1043 showGroupConsensus_actionPerformed(e);
1047 showConsensusHistogram.setText("Show Consensus Histogram");
1048 showConsensusHistogram.addActionListener(new ActionListener()
1051 public void actionPerformed(ActionEvent e)
1053 showConsensusHistogram_actionPerformed(e);
1057 showSequenceLogo.setText("Show Consensus Logo");
1058 showSequenceLogo.addActionListener(new ActionListener()
1061 public void actionPerformed(ActionEvent e)
1063 showSequenceLogo_actionPerformed(e);
1067 applyAutoAnnotationSettings.setText("Apply to all groups");
1068 applyAutoAnnotationSettings.setState(false);
1069 applyAutoAnnotationSettings.setVisible(true);
1070 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1073 public void actionPerformed(ActionEvent e)
1075 applyAutoAnnotationSettings_actionPerformed(e);
1080 nucleotideColour.setText("Nucleotide");
1081 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1083 public void actionPerformed(ActionEvent e)
1085 nucleotideColour_actionPerformed(e);
1088 deleteGroups.setText("Undefine groups");
1089 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1090 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1091 .getMenuShortcutKeyMask(), false));
1092 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1094 public void actionPerformed(ActionEvent e)
1096 deleteGroups_actionPerformed(e);
1099 copy.setText("Copy");
1100 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1101 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1102 .getMenuShortcutKeyMask(), false));
1104 copy.addActionListener(new java.awt.event.ActionListener()
1106 public void actionPerformed(ActionEvent e)
1108 copy_actionPerformed(e);
1112 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1113 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1114 .getMenuShortcutKeyMask(), false));
1115 cut.addActionListener(new java.awt.event.ActionListener()
1117 public void actionPerformed(ActionEvent e)
1119 cut_actionPerformed(e);
1122 delete.setText("Delete");
1123 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1124 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1125 delete.addActionListener(new java.awt.event.ActionListener()
1127 public void actionPerformed(ActionEvent e)
1129 delete_actionPerformed(e);
1132 pasteMenu.setText("Paste");
1133 pasteNew.setText("To New Alignment");
1134 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1135 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1136 .getMenuShortcutKeyMask()
1137 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1138 pasteNew.addActionListener(new java.awt.event.ActionListener()
1140 public void actionPerformed(ActionEvent e)
1142 pasteNew_actionPerformed(e);
1145 pasteThis.setText("Add To This Alignment");
1146 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1147 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1148 .getMenuShortcutKeyMask(), false));
1149 pasteThis.addActionListener(new java.awt.event.ActionListener()
1151 public void actionPerformed(ActionEvent e)
1153 pasteThis_actionPerformed(e);
1156 applyToAllGroups.setText("Apply Colour To All Groups");
1157 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1159 public void actionPerformed(ActionEvent e)
1161 applyToAllGroups_actionPerformed(e);
1164 createPNG.addActionListener(new java.awt.event.ActionListener()
1166 public void actionPerformed(ActionEvent e)
1171 createPNG.setActionCommand("Save As PNG Image");
1172 createPNG.setText("PNG");
1173 font.setText("Font...");
1174 font.addActionListener(new java.awt.event.ActionListener()
1176 public void actionPerformed(ActionEvent e)
1178 font_actionPerformed(e);
1182 seqLimits.setText("Show Sequence Limits");
1183 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1184 seqLimits.addActionListener(new java.awt.event.ActionListener()
1186 public void actionPerformed(ActionEvent e)
1188 seqLimit_actionPerformed(e);
1191 epsFile.setText("EPS");
1192 epsFile.addActionListener(new java.awt.event.ActionListener()
1194 public void actionPerformed(ActionEvent e)
1199 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1200 LoadtreeMenuItem.setText("Load Associated Tree");
1201 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1203 public void actionPerformed(ActionEvent e)
1205 LoadtreeMenuItem_actionPerformed(e);
1208 scaleAbove.setVisible(false);
1209 scaleAbove.setText("Scale Above");
1210 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1212 public void actionPerformed(ActionEvent e)
1214 scaleAbove_actionPerformed(e);
1217 scaleLeft.setVisible(false);
1218 scaleLeft.setSelected(true);
1219 scaleLeft.setText("Scale Left");
1220 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1222 public void actionPerformed(ActionEvent e)
1224 scaleLeft_actionPerformed(e);
1227 scaleRight.setVisible(false);
1228 scaleRight.setSelected(true);
1229 scaleRight.setText("Scale Right");
1230 scaleRight.addActionListener(new java.awt.event.ActionListener()
1232 public void actionPerformed(ActionEvent e)
1234 scaleRight_actionPerformed(e);
1237 centreColumnLabelsMenuItem.setVisible(true);
1238 centreColumnLabelsMenuItem.setState(false);
1239 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1240 centreColumnLabelsMenuItem
1241 .addActionListener(new java.awt.event.ActionListener()
1243 public void actionPerformed(ActionEvent e)
1245 centreColumnLabels_actionPerformed(e);
1248 followHighlightMenuItem.setVisible(true);
1249 followHighlightMenuItem.setState(true);
1250 followHighlightMenuItem.setText("Automatic Scrolling");
1251 followHighlightMenuItem.addActionListener(new ActionListener()
1254 public void actionPerformed(ActionEvent e)
1256 followHighlight_actionPerformed();
1261 modifyPID.setText("Modify Identity Threshold...");
1262 modifyPID.addActionListener(new java.awt.event.ActionListener()
1264 public void actionPerformed(ActionEvent e)
1266 modifyPID_actionPerformed(e);
1269 modifyConservation.setText("Modify Conservation Threshold...");
1271 .addActionListener(new java.awt.event.ActionListener()
1273 public void actionPerformed(ActionEvent e)
1275 modifyConservation_actionPerformed(e);
1278 sortByTreeMenu.setText("By Tree Order");
1279 sort.setText("Sort");
1280 sort.addMenuListener(new MenuListener()
1282 public void menuSelected(MenuEvent e)
1287 public void menuDeselected(MenuEvent e)
1291 public void menuCanceled(MenuEvent e)
1295 sortByAnnotScore.setText("by Score");
1296 sort.add(sortByAnnotScore);
1297 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1300 public void menuCanceled(MenuEvent e)
1304 public void menuDeselected(MenuEvent e)
1308 public void menuSelected(MenuEvent e)
1310 buildSortByAnnotationScoresMenu();
1313 sortByAnnotScore.setVisible(false);
1315 calculateTree.setText("Calculate Tree");
1317 jMenu2.setText("Export Image");
1318 padGapsMenuitem.setText("Pad Gaps");
1319 padGapsMenuitem.setState(jalview.bin.Cache
1320 .getDefault("PAD_GAPS", false));
1321 padGapsMenuitem.addActionListener(new ActionListener()
1323 public void actionPerformed(ActionEvent e)
1325 padGapsMenuitem_actionPerformed(e);
1328 vamsasStore.setVisible(false);
1329 vamsasStore.setText("VAMSAS store");
1330 vamsasStore.addActionListener(new ActionListener()
1332 public void actionPerformed(ActionEvent e)
1334 vamsasStore_actionPerformed(e);
1337 showTranslation.setText("Translate cDNA");
1338 showTranslation.addActionListener(new ActionListener()
1340 public void actionPerformed(ActionEvent e)
1342 showTranslation_actionPerformed(e);
1345 extractScores.setText("Extract Scores...");
1346 extractScores.addActionListener(new ActionListener()
1348 public void actionPerformed(ActionEvent e)
1350 extractScores_actionPerformed(e);
1353 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1355 showProducts.setText("Get Cross References");
1357 * showProducts.addActionListener(new ActionListener() {
1359 * public void actionPerformed(ActionEvent e) {
1360 * showProducts_actionPerformed(e); } });
1362 featureSettings.setText("Feature Settings...");
1363 featureSettings.addActionListener(new ActionListener()
1365 public void actionPerformed(ActionEvent e)
1367 featureSettings_actionPerformed(e);
1370 fetchSequence.setText("Fetch Sequence(s)...");
1371 fetchSequence.addActionListener(new ActionListener()
1373 public void actionPerformed(ActionEvent e)
1375 fetchSequence_actionPerformed(e);
1379 annotationColour.setText("By Annotation...");
1380 annotationColour.addActionListener(new ActionListener()
1382 public void actionPerformed(ActionEvent e)
1384 annotationColour_actionPerformed(e);
1387 associatedData.setText("Load Features / Annotations");
1388 associatedData.addActionListener(new ActionListener()
1390 public void actionPerformed(ActionEvent e)
1392 associatedData_actionPerformed(e);
1395 autoCalculate.setText("Autocalculate Consensus");
1396 autoCalculate.setState(jalview.bin.Cache.getDefault(
1397 "AUTO_CALC_CONSENSUS", true));
1398 autoCalculate.addActionListener(new ActionListener()
1400 public void actionPerformed(ActionEvent e)
1402 autoCalculate_actionPerformed(e);
1405 addSequenceMenu.setText("Add Sequences");
1406 addFromFile.setText("From File");
1407 addFromFile.addActionListener(new ActionListener()
1409 public void actionPerformed(ActionEvent e)
1411 addFromFile_actionPerformed(e);
1414 addFromText.setText("From Textbox");
1415 addFromText.addActionListener(new ActionListener()
1417 public void actionPerformed(ActionEvent e)
1419 addFromText_actionPerformed(e);
1422 addFromURL.setText("From URL");
1423 addFromURL.addActionListener(new ActionListener()
1425 public void actionPerformed(ActionEvent e)
1427 addFromURL_actionPerformed(e);
1430 exportFeatures.setText("Export Features...");
1431 exportFeatures.addActionListener(new ActionListener()
1433 public void actionPerformed(ActionEvent e)
1435 exportFeatures_actionPerformed(e);
1438 exportAnnotations.setText("Export Annotations...");
1439 exportAnnotations.addActionListener(new ActionListener()
1441 public void actionPerformed(ActionEvent e)
1443 exportAnnotations_actionPerformed(e);
1446 statusPanel.setLayout(gridLayout1);
1447 jMenu3.setText("Show");
1448 showAllSeqs.setText("All Sequences");
1449 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1450 showAllSeqs.addActionListener(new ActionListener()
1452 public void actionPerformed(ActionEvent e)
1454 showAllSeqs_actionPerformed(e);
1457 showAllColumns.setText("All Columns");
1458 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1459 showAllColumns.addActionListener(new ActionListener()
1461 public void actionPerformed(ActionEvent e)
1463 showAllColumns_actionPerformed(e);
1466 hideMenu.setText("Hide");
1467 hideSelSequences.setText("Selected Sequences");
1468 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1469 hideSelSequences.addActionListener(new ActionListener()
1471 public void actionPerformed(ActionEvent e)
1473 hideSelSequences_actionPerformed(e);
1476 hideSelColumns.setText("Selected Columns");
1477 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1478 hideSelColumns.addActionListener(new ActionListener()
1480 public void actionPerformed(ActionEvent e)
1482 hideSelColumns_actionPerformed(e);
1485 hideAllSelection.setText("Selected Region");
1486 hideAllSelection.addActionListener(new ActionListener()
1488 public void actionPerformed(ActionEvent e)
1490 hideAllSelection_actionPerformed(e);
1493 // TODO: should be hidden if no selection exists.
1494 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1495 hideAllButSelection.addActionListener(new ActionListener()
1497 public void actionPerformed(ActionEvent e)
1499 hideAllButSelection_actionPerformed(e);
1502 showAllhidden.setText("All Sequences and Columns");
1504 .setToolTipText("H toggles visibility of hidden or selected regions.");
1505 showAllhidden.addActionListener(new ActionListener()
1507 public void actionPerformed(ActionEvent e)
1509 showAllhidden_actionPerformed(e);
1513 hiddenMarkers.setText("Show Hidden Markers");
1514 hiddenMarkers.addActionListener(new ActionListener()
1516 public void actionPerformed(ActionEvent e)
1518 hiddenMarkers_actionPerformed(e);
1521 invertColSel.setText("Invert Column Selection");
1522 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1523 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1524 .getMenuShortcutKeyMask()
1525 | java.awt.event.KeyEvent.ALT_MASK, false));
1526 invertColSel.addActionListener(new ActionListener()
1528 public void actionPerformed(ActionEvent e)
1530 invertColSel_actionPerformed(e);
1533 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1535 public void stateChanged(ChangeEvent evt)
1537 JTabbedPane pane = (JTabbedPane) evt.getSource();
1538 int sel = pane.getSelectedIndex();
1539 tabSelectionChanged(sel);
1542 tabbedPane.addMouseListener(new MouseAdapter()
1544 public void mousePressed(MouseEvent e)
1546 tabbedPane_mousePressed(e);
1549 tabbedPane.addFocusListener(new FocusAdapter()
1551 public void focusGained(FocusEvent e)
1553 tabbedPane_focusGained(e);
1556 save.setText("Save");
1557 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1558 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1559 .getMenuShortcutKeyMask(), false));
1560 save.addActionListener(new ActionListener()
1562 public void actionPerformed(ActionEvent e)
1564 save_actionPerformed(e);
1567 reload.setEnabled(false);
1568 reload.setText("Reload");
1569 reload.addActionListener(new ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 reload_actionPerformed(e);
1576 newView.setText("New View");
1577 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1578 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1579 .getMenuShortcutKeyMask(), false));
1580 newView.addActionListener(new ActionListener()
1582 public void actionPerformed(ActionEvent e)
1584 newView_actionPerformed(e);
1587 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1588 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1589 textColour.setText("Colour Text ...");
1590 textColour.addActionListener(new ActionListener()
1592 public void actionPerformed(ActionEvent e)
1594 textColour_actionPerformed(e);
1597 formatMenu.setText("Format");
1598 selectMenu.setText("Select");
1599 idRightAlign.setText("Right Align Sequence Id");
1600 idRightAlign.addActionListener(new ActionListener()
1602 public void actionPerformed(ActionEvent e)
1604 idRightAlign_actionPerformed(e);
1607 gatherViews.setEnabled(false);
1608 gatherViews.setText("Gather Views");
1609 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1610 java.awt.event.KeyEvent.VK_G, 0, false));
1611 gatherViews.addActionListener(new ActionListener()
1613 public void actionPerformed(ActionEvent e)
1615 gatherViews_actionPerformed(e);
1618 expandViews.setEnabled(false);
1619 expandViews.setText("Expand Views");
1620 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1621 java.awt.event.KeyEvent.VK_X, 0, false));
1622 expandViews.addActionListener(new ActionListener()
1624 public void actionPerformed(ActionEvent e)
1626 expandViews_actionPerformed(e);
1629 pageSetup.setText("Page Setup ...");
1630 pageSetup.addActionListener(new ActionListener()
1632 public void actionPerformed(ActionEvent e)
1634 pageSetup_actionPerformed(e);
1637 alignmentProperties.setText("Alignment Properties...");
1638 alignmentProperties.addActionListener(new ActionListener()
1640 public void actionPerformed(ActionEvent actionEvent)
1642 alignmentProperties();
1645 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1646 autoAnnMenu.setText("Autocalculated Annotation");
1647 alignFrameMenuBar.add(fileMenu);
1648 alignFrameMenuBar.add(editMenu);
1649 alignFrameMenuBar.add(selectMenu);
1650 alignFrameMenuBar.add(viewMenu);
1651 alignFrameMenuBar.add(formatMenu);
1652 alignFrameMenuBar.add(colourMenu);
1653 alignFrameMenuBar.add(calculateMenu);
1654 alignFrameMenuBar.add(webService);
1655 fileMenu.add(fetchSequence);
1656 fileMenu.add(addSequenceMenu);
1657 fileMenu.add(reload);
1658 fileMenu.addSeparator();
1659 fileMenu.add(vamsasStore);
1661 fileMenu.add(saveAs);
1662 fileMenu.add(outputTextboxMenu);
1663 fileMenu.add(pageSetup);
1664 fileMenu.add(printMenuItem);
1665 fileMenu.addSeparator();
1666 fileMenu.add(jMenu2);
1667 fileMenu.add(exportFeatures);
1668 fileMenu.add(exportAnnotations);
1669 fileMenu.add(LoadtreeMenuItem);
1670 fileMenu.add(associatedData);
1671 fileMenu.addSeparator();
1672 fileMenu.add(closeMenuItem);
1673 editMenu.add(undoMenuItem);
1674 editMenu.add(redoMenuItem);
1677 editMenu.add(pasteMenu);
1678 editMenu.add(delete);
1679 editMenu.addSeparator();
1680 editMenu.add(remove2LeftMenuItem);
1681 editMenu.add(remove2RightMenuItem);
1682 editMenu.add(removeGappedColumnMenuItem);
1683 editMenu.add(removeAllGapsMenuItem);
1684 editMenu.add(removeRedundancyMenuItem);
1685 editMenu.addSeparator();
1686 // dont add these yet in the CVS build - they cannot be undone!
1687 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1688 // editMenu.add(justifyLeftMenuItem);
1689 // editMenu.add(justifyRightMenuItem);
1690 // editMenu.addSeparator();
1691 editMenu.add(padGapsMenuitem);
1692 viewMenu.add(newView);
1693 viewMenu.add(expandViews);
1694 viewMenu.add(gatherViews);
1695 viewMenu.addSeparator();
1696 viewMenu.add(jMenu3);
1697 viewMenu.add(hideMenu);
1698 viewMenu.addSeparator();
1699 viewMenu.add(followHighlightMenuItem);
1700 viewMenu.add(annotationPanelMenuItem);
1701 autoAnnMenu.add(applyAutoAnnotationSettings);
1702 autoAnnMenu.add(showConsensusHistogram);
1703 autoAnnMenu.add(showSequenceLogo);
1704 autoAnnMenu.addSeparator();
1705 autoAnnMenu.add(showGroupConservation);
1706 autoAnnMenu.add(showGroupConsensus);
1707 viewMenu.add(autoAnnMenu);
1708 viewMenu.addSeparator();
1709 viewMenu.add(showSeqFeatures);
1710 // viewMenu.add(showSeqFeaturesHeight);
1712 viewMenu.add(featureSettings);
1713 tooltipSettingsMenu.add(showDbRefsMenuitem);
1714 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1715 viewMenu.add(tooltipSettingsMenu);
1716 viewMenu.addSeparator();
1717 viewMenu.add(alignmentProperties);
1718 viewMenu.addSeparator();
1719 viewMenu.add(overviewMenuItem);
1720 colourMenu.add(applyToAllGroups);
1721 colourMenu.add(textColour);
1722 colourMenu.addSeparator();
1723 colourMenu.add(noColourmenuItem);
1724 colourMenu.add(clustalColour);
1725 colourMenu.add(BLOSUM62Colour);
1726 colourMenu.add(PIDColour);
1727 colourMenu.add(zappoColour);
1728 colourMenu.add(taylorColour);
1729 colourMenu.add(hydrophobicityColour);
1730 colourMenu.add(helixColour);
1731 colourMenu.add(strandColour);
1732 colourMenu.add(turnColour);
1733 colourMenu.add(buriedColour);
1734 colourMenu.add(nucleotideColour);
1735 colourMenu.add(userDefinedColour);
1736 colourMenu.addSeparator();
1737 colourMenu.add(conservationMenuItem);
1738 colourMenu.add(modifyConservation);
1739 colourMenu.add(abovePIDThreshold);
1740 colourMenu.add(modifyPID);
1741 colourMenu.add(annotationColour);
1742 calculateMenu.add(sort);
1743 calculateMenu.add(calculateTree);
1744 calculateMenu.addSeparator();
1745 calculateMenu.add(pairwiseAlignmentMenuItem);
1746 calculateMenu.add(PCAMenuItem);
1747 calculateMenu.addSeparator();
1748 calculateMenu.add(showTranslation);
1749 calculateMenu.add(showProducts);
1750 calculateMenu.add(autoCalculate);
1751 calculateMenu.addSeparator();
1752 calculateMenu.add(extractScores);
1753 webServiceNoServices = new JMenuItem("<No Services>");
1754 webService.add(webServiceNoServices);
1755 pasteMenu.add(pasteNew);
1756 pasteMenu.add(pasteThis);
1757 sort.add(sortIDMenuItem);
1758 sort.add(sortLengthMenuItem);
1759 sort.add(sortGroupMenuItem);
1760 sort.add(sortPairwiseMenuItem);
1761 sort.add(sortByTreeMenu);
1762 calculateTree.add(averageDistanceTreeMenuItem);
1763 calculateTree.add(neighbourTreeMenuItem);
1764 calculateTree.add(avDistanceTreeBlosumMenuItem);
1765 calculateTree.add(njTreeBlosumMenuItem);
1766 jMenu2.add(htmlMenuItem);
1767 jMenu2.add(epsFile);
1768 jMenu2.add(createPNG);
1769 addSequenceMenu.add(addFromFile);
1770 addSequenceMenu.add(addFromText);
1771 addSequenceMenu.add(addFromURL);
1772 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1773 statusPanel.add(statusBar, null);
1774 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1775 jMenu3.add(showAllColumns);
1776 jMenu3.add(showAllSeqs);
1777 jMenu3.add(showAllhidden);
1778 hideMenu.add(hideSelColumns);
1779 hideMenu.add(hideSelSequences);
1780 hideMenu.add(hideAllSelection);
1781 hideMenu.add(hideAllButSelection);
1783 formatMenu.add(font);
1784 formatMenu.addSeparator();
1785 formatMenu.add(wrapMenuItem);
1786 formatMenu.add(scaleAbove);
1787 formatMenu.add(scaleLeft);
1788 formatMenu.add(scaleRight);
1789 formatMenu.add(seqLimits);
1790 formatMenu.add(idRightAlign);
1791 formatMenu.add(hiddenMarkers);
1792 formatMenu.add(viewBoxesMenuItem);
1793 formatMenu.add(viewTextMenuItem);
1794 formatMenu.add(colourTextMenuItem);
1795 formatMenu.add(renderGapsMenuItem);
1796 formatMenu.add(centreColumnLabelsMenuItem);
1797 formatMenu.add(showNonconservedMenuItem);
1798 selectMenu.add(findMenuItem);
1799 selectMenu.addSeparator();
1800 selectMenu.add(selectAllSequenceMenuItem);
1801 selectMenu.add(deselectAllSequenceMenuItem);
1802 selectMenu.add(invertSequenceMenuItem);
1803 selectMenu.add(invertColSel);
1804 selectMenu.add(deleteGroups);
1805 selectMenu.add(grpsFromSelection);
1808 protected void showAllhidden_actionPerformed(ActionEvent e)
1810 // TODO Auto-generated method stub
1814 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1816 // TODO Auto-generated method stub
1820 protected void hideAllSelection_actionPerformed(ActionEvent e)
1822 // TODO Auto-generated method stub
1826 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1828 // TODO Auto-generated method stub
1832 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1834 // TODO Auto-generated method stub
1838 protected void showSequenceLogo_actionPerformed(ActionEvent e)
1840 // TODO Auto-generated method stub
1844 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1846 // TODO Auto-generated method stub
1850 protected void showGroupConsensus_actionPerformed(ActionEvent e)
1852 // TODO Auto-generated method stub
1856 protected void showGroupConservation_actionPerformed(ActionEvent e)
1858 // TODO Auto-generated method stub
1862 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1864 // TODO Auto-generated method stub
1868 protected void showSeqFeaturesHeight_actionPerformed(
1869 ActionEvent actionEvent)
1871 // TODO Auto-generated method stub
1875 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1877 // TODO Auto-generated method stub
1881 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1883 // TODO Auto-generated method stub
1887 protected void followHighlight_actionPerformed()
1889 // TODO Auto-generated method stub
1893 protected void showNpFeats_actionPerformed(ActionEvent e)
1895 // TODO Auto-generated method stub
1899 protected void showDbRefs_actionPerformed(ActionEvent e)
1901 // TODO Auto-generated method stub
1905 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1909 protected void showProducts_actionPerformed(ActionEvent e)
1913 protected void buildSortByAnnotationScoresMenu()
1917 protected void extractScores_actionPerformed(ActionEvent e)
1921 protected void outputText_actionPerformed(ActionEvent e)
1925 public void addFromFile_actionPerformed(ActionEvent e)
1930 public void addFromText_actionPerformed(ActionEvent e)
1935 public void addFromURL_actionPerformed(ActionEvent e)
1940 public void exportFeatures_actionPerformed(ActionEvent e)
1945 public void exportAnnotations_actionPerformed(ActionEvent e)
1950 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1954 protected void closeMenuItem_actionPerformed(boolean b)
1958 protected void redoMenuItem_actionPerformed(ActionEvent e)
1962 protected void undoMenuItem_actionPerformed(ActionEvent e)
1966 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1970 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1974 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1978 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1982 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1986 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1990 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1994 protected void wrapMenuItem_actionPerformed(ActionEvent e)
1998 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2002 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2006 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2010 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2014 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2018 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2022 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2026 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2030 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2034 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2038 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2042 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2046 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2050 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2054 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2058 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2062 protected void clustalColour_actionPerformed(ActionEvent e)
2066 protected void zappoColour_actionPerformed(ActionEvent e)
2070 protected void taylorColour_actionPerformed(ActionEvent e)
2074 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2078 protected void helixColour_actionPerformed(ActionEvent e)
2082 protected void strandColour_actionPerformed(ActionEvent e)
2086 protected void turnColour_actionPerformed(ActionEvent e)
2090 protected void buriedColour_actionPerformed(ActionEvent e)
2094 protected void userDefinedColour_actionPerformed(ActionEvent e)
2098 protected void PIDColour_actionPerformed(ActionEvent e)
2102 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2106 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2110 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2114 protected void printMenuItem_actionPerformed(ActionEvent e)
2118 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2122 protected void findMenuItem_actionPerformed(ActionEvent e)
2126 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2130 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2134 protected void nucleotideColour_actionPerformed(ActionEvent e)
2138 protected void deleteGroups_actionPerformed(ActionEvent e)
2142 protected void copy_actionPerformed(ActionEvent e)
2146 protected void cut_actionPerformed(ActionEvent e)
2150 protected void delete_actionPerformed(ActionEvent e)
2154 protected void pasteNew_actionPerformed(ActionEvent e)
2158 protected void pasteThis_actionPerformed(ActionEvent e)
2162 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2166 public void createPNG(java.io.File f)
2170 protected void font_actionPerformed(ActionEvent e)
2174 protected void seqLimit_actionPerformed(ActionEvent e)
2178 public void seqDBRef_actionPerformed(ActionEvent e)
2183 public void createEPS(java.io.File f)
2187 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2191 protected void jpred_actionPerformed(ActionEvent e)
2195 protected void scaleAbove_actionPerformed(ActionEvent e)
2199 protected void scaleLeft_actionPerformed(ActionEvent e)
2203 protected void scaleRight_actionPerformed(ActionEvent e)
2207 protected void modifyPID_actionPerformed(ActionEvent e)
2211 protected void modifyConservation_actionPerformed(ActionEvent e)
2215 protected void saveAs_actionPerformed(ActionEvent e)
2219 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2223 public void vamsasStore_actionPerformed(ActionEvent e)
2228 public void vamsasLoad_actionPerformed(ActionEvent e)
2233 public void showTranslation_actionPerformed(ActionEvent e)
2238 public void featureSettings_actionPerformed(ActionEvent e)
2243 public void fetchSequence_actionPerformed(ActionEvent e)
2248 public void smoothFont_actionPerformed(ActionEvent e)
2253 public void annotationColour_actionPerformed(ActionEvent e)
2258 public void associatedData_actionPerformed(ActionEvent e)
2263 public void autoCalculate_actionPerformed(ActionEvent e)
2268 public void showAllSeqs_actionPerformed(ActionEvent e)
2273 public void showAllColumns_actionPerformed(ActionEvent e)
2278 public void hideSelSequences_actionPerformed(ActionEvent e)
2283 public void hideSelColumns_actionPerformed(ActionEvent e)
2288 public void hiddenMarkers_actionPerformed(ActionEvent e)
2293 public void findPdbId_actionPerformed(ActionEvent e)
2298 public void enterPdbId_actionPerformed(ActionEvent e)
2303 public void pdbFile_actionPerformed(ActionEvent e)
2308 public void invertColSel_actionPerformed(ActionEvent e)
2313 public void tabSelectionChanged(int sel)
2318 public void tabbedPane_mousePressed(MouseEvent e)
2323 public void tabbedPane_focusGained(FocusEvent e)
2328 public void save_actionPerformed(ActionEvent e)
2333 public void reload_actionPerformed(ActionEvent e)
2338 public void newView_actionPerformed(ActionEvent e)
2343 public void textColour_actionPerformed(ActionEvent e)
2348 public void idRightAlign_actionPerformed(ActionEvent e)
2353 public void expandViews_actionPerformed(ActionEvent e)
2358 public void gatherViews_actionPerformed(ActionEvent e)
2363 public void buildTreeMenu()
2368 public void pageSetup_actionPerformed(ActionEvent e)
2373 public void alignmentProperties()