2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.jbgui;
22 import java.awt.event.*;
25 import javax.swing.event.*;
27 import jalview.schemes.*;
29 public class GAlignFrame extends JInternalFrame
31 protected JMenuBar alignFrameMenuBar = new JMenuBar();
33 protected JMenu fileMenu = new JMenu();
35 protected JMenuItem closeMenuItem = new JMenuItem();
37 protected JMenu editMenu = new JMenu();
39 protected JMenu viewMenu = new JMenu();
41 protected JMenu colourMenu = new JMenu();
43 protected JMenu calculateMenu = new JMenu();
45 protected JMenu webService = new JMenu();
47 protected JMenuItem webServiceNoServices;
49 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
51 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
53 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
55 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
57 protected JMenuItem remove2RightMenuItem = new JMenuItem();
59 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
61 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
63 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
65 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
67 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
69 protected JMenuItem sortIDMenuItem = new JMenuItem();
71 protected JMenuItem sortLengthMenuItem = new JMenuItem();
73 protected JMenuItem sortGroupMenuItem = new JMenuItem();
75 protected JMenu sortByAnnotScore = new JMenu();
77 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
79 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
81 protected JMenuItem PCAMenuItem = new JMenuItem();
83 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
85 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
87 BorderLayout borderLayout1 = new BorderLayout();
89 public JLabel statusBar = new JLabel();
91 protected JMenuItem saveAs = new JMenuItem();
93 protected JMenu outputTextboxMenu = new JMenu();
95 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
97 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
99 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
101 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
103 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
105 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
107 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
109 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
111 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
113 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
115 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
117 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
119 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
121 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
123 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
125 public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
127 JMenuItem htmlMenuItem = new JMenuItem();
129 JMenuItem overviewMenuItem = new JMenuItem();
131 protected JMenuItem undoMenuItem = new JMenuItem();
133 protected JMenuItem redoMenuItem = new JMenuItem();
135 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
137 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
139 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
141 JMenuItem printMenuItem = new JMenuItem();
143 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
145 JMenuItem findMenuItem = new JMenuItem();
147 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
149 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();
199 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
200 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
202 protected ButtonGroup colours = new ButtonGroup();
204 JMenuItem vamsasStore = new JMenuItem();
206 protected JMenuItem showTranslation = new JMenuItem();
208 protected JMenuItem extractScores = new JMenuItem();
210 protected JMenu showProducts = new JMenu();
212 public JMenuItem featureSettings = new JMenuItem();
214 JMenuItem fetchSequence = new JMenuItem();
216 JMenuItem annotationColour = new JMenuItem();
218 JMenuItem associatedData = new JMenuItem();
220 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
222 JMenu addSequenceMenu = new JMenu();
224 JMenuItem addFromFile = new JMenuItem();
226 JMenuItem addFromText = new JMenuItem();
228 JMenuItem addFromURL = new JMenuItem();
230 JMenuItem exportAnnotations = new JMenuItem();
232 JMenuItem exportFeatures = new JMenuItem();
234 protected JPanel statusPanel = new JPanel();
236 GridLayout gridLayout1 = new GridLayout();
238 JMenu jMenu3 = new JMenu();
240 JMenuItem showAllSeqs = new JMenuItem();
242 JMenuItem showAllColumns = new JMenuItem();
244 JMenu hideMenu = new JMenu();
246 JMenuItem hideSelSequences = new JMenuItem();
248 JMenuItem hideSelColumns = new JMenuItem();
250 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
252 JMenuItem invertColSel = new JMenuItem();
254 protected JTabbedPane tabbedPane = new JTabbedPane();
256 JMenuItem save = new JMenuItem();
258 protected JMenuItem reload = new JMenuItem();
260 JMenuItem newView = new JMenuItem();
262 JMenuItem textColour = new JMenuItem();
264 JMenu formatMenu = new JMenu();
266 JMenu selectMenu = new JMenu();
268 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
270 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
272 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
274 protected JMenuItem gatherViews = new JMenuItem();
276 protected JMenuItem expandViews = new JMenuItem();
278 JMenuItem pageSetup = new JMenuItem();
280 JMenuItem alignmentProperties = new JMenuItem();
282 JMenu tooltipSettingsMenu = new JMenu();
284 private JMenuItem justifyLeftMenuItem=new JMenuItem();
286 private JMenuItem justifyRightMenuItem=new JMenuItem();
288 JMenu autoAnnMenu = new JMenu();
289 protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
290 protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
291 protected JCheckBoxMenuItem showConsensusHistogram=new JCheckBoxMenuItem();
292 protected JCheckBoxMenuItem showConsensusProfile=new JCheckBoxMenuItem();
293 protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem();
295 private JMenuItem grpsFromSelection = new JMenuItem();
301 setJMenuBar(alignFrameMenuBar);
303 // dynamically fill save as menu with available formats
304 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
306 JMenuItem item = new JMenuItem(
307 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
309 item.addActionListener(new java.awt.event.ActionListener()
311 public void actionPerformed(ActionEvent e)
313 outputText_actionPerformed(e);
317 outputTextboxMenu.add(item);
319 } catch (Exception e)
323 if (!new jalview.util.Platform().isAMac())
325 closeMenuItem.setMnemonic('C');
326 outputTextboxMenu.setMnemonic('T');
327 undoMenuItem.setMnemonic('Z');
328 redoMenuItem.setMnemonic('0');
329 copy.setMnemonic('C');
330 cut.setMnemonic('U');
331 pasteMenu.setMnemonic('P');
332 reload.setMnemonic('R');
335 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
337 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
338 .getUserColourSchemes().keys();
340 while (userColours.hasMoreElements())
342 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
343 userColours.nextElement().toString());
344 radioItem.setName("USER_DEFINED");
345 radioItem.addMouseListener(new MouseAdapter()
347 public void mousePressed(MouseEvent evt)
349 if (evt.isControlDown()
350 || SwingUtilities.isRightMouseButton(evt))
353 .removeActionListener(radioItem.getActionListeners()[0]);
355 int option = JOptionPane.showInternalConfirmDialog(
356 jalview.gui.Desktop.desktop,
357 "Remove from default list?",
358 "Remove user defined colour",
359 JOptionPane.YES_NO_OPTION);
360 if (option == JOptionPane.YES_OPTION)
362 jalview.gui.UserDefinedColours
363 .removeColourFromDefaults(radioItem.getText());
364 colourMenu.remove(radioItem);
368 radioItem.addActionListener(new ActionListener()
370 public void actionPerformed(ActionEvent evt)
372 userDefinedColour_actionPerformed(evt);
379 radioItem.addActionListener(new ActionListener()
381 public void actionPerformed(ActionEvent evt)
383 userDefinedColour_actionPerformed(evt);
386 colourMenu.insert(radioItem, 15);
387 colours.add(radioItem);
390 colours.add(noColourmenuItem);
391 colours.add(clustalColour);
392 colours.add(zappoColour);
393 colours.add(taylorColour);
394 colours.add(hydrophobicityColour);
395 colours.add(helixColour);
396 colours.add(strandColour);
397 colours.add(turnColour);
398 colours.add(buriedColour);
399 colours.add(userDefinedColour);
400 colours.add(PIDColour);
401 colours.add(BLOSUM62Colour);
402 colours.add(nucleotideColour);
404 setColourSelected(jalview.bin.Cache
405 .getDefault("DEFAULT_COLOUR", "None"));
409 public void setColourSelected(String defaultColour)
412 if (defaultColour != null)
414 int index = ColourSchemeProperty
415 .getColourIndexFromName(defaultColour);
419 case ColourSchemeProperty.NONE:
420 noColourmenuItem.setSelected(true);
422 case ColourSchemeProperty.CLUSTAL:
423 clustalColour.setSelected(true);
427 case ColourSchemeProperty.BLOSUM:
428 BLOSUM62Colour.setSelected(true);
432 case ColourSchemeProperty.PID:
433 PIDColour.setSelected(true);
437 case ColourSchemeProperty.ZAPPO:
438 zappoColour.setSelected(true);
442 case ColourSchemeProperty.TAYLOR:
443 taylorColour.setSelected(true);
446 case ColourSchemeProperty.HYDROPHOBIC:
447 hydrophobicityColour.setSelected(true);
451 case ColourSchemeProperty.HELIX:
452 helixColour.setSelected(true);
456 case ColourSchemeProperty.STRAND:
457 strandColour.setSelected(true);
461 case ColourSchemeProperty.TURN:
462 turnColour.setSelected(true);
466 case ColourSchemeProperty.BURIED:
467 buriedColour.setSelected(true);
471 case ColourSchemeProperty.NUCLEOTIDE:
472 nucleotideColour.setSelected(true);
476 case ColourSchemeProperty.USER_DEFINED:
477 userDefinedColour.setSelected(true);
485 private void jbInit() throws Exception
487 fileMenu.setText("File");
488 saveAs.setText("Save As...");
489 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
490 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
491 .getMenuShortcutKeyMask()
492 | java.awt.event.KeyEvent.SHIFT_MASK, false));
493 saveAs.addActionListener(new ActionListener()
495 public void actionPerformed(ActionEvent e)
497 saveAs_actionPerformed(e);
500 closeMenuItem.setText("Close");
501 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
502 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
503 .getMenuShortcutKeyMask(), false));
504 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
506 public void actionPerformed(ActionEvent e)
508 closeMenuItem_actionPerformed(false);
511 editMenu.setText("Edit");
512 viewMenu.setText("View");
513 colourMenu.setText("Colour");
514 calculateMenu.setText("Calculate");
515 webService.setText("Web Service");
516 selectAllSequenceMenuItem.setText("Select All");
517 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
518 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
519 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
520 selectAllSequenceMenuItem
521 .addActionListener(new java.awt.event.ActionListener()
523 public void actionPerformed(ActionEvent e)
525 selectAllSequenceMenuItem_actionPerformed(e);
528 deselectAllSequenceMenuItem.setText("Deselect All");
529 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
530 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
531 deselectAllSequenceMenuItem
532 .addActionListener(new java.awt.event.ActionListener()
534 public void actionPerformed(ActionEvent e)
536 deselectAllSequenceMenuItem_actionPerformed(e);
539 invertSequenceMenuItem.setText("Invert Sequence Selection");
540 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
541 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
542 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
543 invertSequenceMenuItem
544 .addActionListener(new java.awt.event.ActionListener()
546 public void actionPerformed(ActionEvent e)
548 invertSequenceMenuItem_actionPerformed(e);
551 grpsFromSelection.setText("Make Groups for selection");
552 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
554 public void actionPerformed(ActionEvent e)
556 makeGrpsFromSelection_actionPerformed(e);
560 remove2LeftMenuItem.setText("Remove Left");
561 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
562 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
563 .getMenuShortcutKeyMask(), false));
565 .addActionListener(new java.awt.event.ActionListener()
567 public void actionPerformed(ActionEvent e)
569 remove2LeftMenuItem_actionPerformed(e);
572 remove2RightMenuItem.setText("Remove Right");
573 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
574 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
575 .getMenuShortcutKeyMask(), false));
577 .addActionListener(new java.awt.event.ActionListener()
579 public void actionPerformed(ActionEvent e)
581 remove2RightMenuItem_actionPerformed(e);
584 removeGappedColumnMenuItem.setText("Remove Empty Columns");
585 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
586 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
587 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
588 removeGappedColumnMenuItem
589 .addActionListener(new java.awt.event.ActionListener()
591 public void actionPerformed(ActionEvent e)
593 removeGappedColumnMenuItem_actionPerformed(e);
596 removeAllGapsMenuItem.setText("Remove All Gaps");
597 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
598 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
599 .getDefaultToolkit().getMenuShortcutKeyMask()
600 | java.awt.event.KeyEvent.SHIFT_MASK, false));
601 removeAllGapsMenuItem
602 .addActionListener(new java.awt.event.ActionListener()
604 public void actionPerformed(ActionEvent e)
606 removeAllGapsMenuItem_actionPerformed(e);
609 justifyLeftMenuItem.setText("Left Justify Alignment");
610 justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
612 public void actionPerformed(ActionEvent e)
614 justifyLeftMenuItem_actionPerformed(e);
617 justifyRightMenuItem.setText("Right Justify Alignment");
618 justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
620 public void actionPerformed(ActionEvent e)
622 justifyRightMenuItem_actionPerformed(e);
625 viewBoxesMenuItem.setText("Boxes");
626 viewBoxesMenuItem.setState(true);
627 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
629 public void actionPerformed(ActionEvent e)
631 viewBoxesMenuItem_actionPerformed(e);
634 viewTextMenuItem.setText("Text");
635 viewTextMenuItem.setState(true);
636 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
638 public void actionPerformed(ActionEvent e)
640 viewTextMenuItem_actionPerformed(e);
643 showUnconservedMenuItem.setText("Show Unconserved");
644 showUnconservedMenuItem.setState(false);
645 showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
647 public void actionPerformed(ActionEvent e)
649 showUnconservedMenuItem_actionPerformed(e);
652 sortPairwiseMenuItem.setText("by Pairwise Identity");
654 .addActionListener(new java.awt.event.ActionListener()
656 public void actionPerformed(ActionEvent e)
658 sortPairwiseMenuItem_actionPerformed(e);
661 sortIDMenuItem.setText("by ID");
662 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
664 public void actionPerformed(ActionEvent e)
666 sortIDMenuItem_actionPerformed(e);
669 sortLengthMenuItem.setText("By Length");
670 sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
672 public void actionPerformed(ActionEvent e)
674 sortLengthMenuItem_actionPerformed(e);
677 sortGroupMenuItem.setText("by Group");
678 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
680 public void actionPerformed(ActionEvent e)
682 sortGroupMenuItem_actionPerformed(e);
685 removeRedundancyMenuItem.setText("Remove Redundancy...");
686 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
687 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
688 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
689 removeRedundancyMenuItem
690 .addActionListener(new java.awt.event.ActionListener()
692 public void actionPerformed(ActionEvent e)
694 removeRedundancyMenuItem_actionPerformed(e);
697 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
698 pairwiseAlignmentMenuItem
699 .addActionListener(new java.awt.event.ActionListener()
701 public void actionPerformed(ActionEvent e)
703 pairwiseAlignmentMenuItem_actionPerformed(e);
706 PCAMenuItem.setText("Principal Component Analysis");
707 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
709 public void actionPerformed(ActionEvent e)
711 PCAMenuItem_actionPerformed(e);
714 averageDistanceTreeMenuItem
715 .setText("Average Distance Using % Identity");
716 averageDistanceTreeMenuItem
717 .addActionListener(new java.awt.event.ActionListener()
719 public void actionPerformed(ActionEvent e)
721 averageDistanceTreeMenuItem_actionPerformed(e);
724 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
725 neighbourTreeMenuItem
726 .addActionListener(new java.awt.event.ActionListener()
728 public void actionPerformed(ActionEvent e)
730 neighbourTreeMenuItem_actionPerformed(e);
733 this.getContentPane().setLayout(borderLayout1);
734 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
735 statusBar.setBackground(Color.white);
736 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
737 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
738 statusBar.setText("Status bar");
739 outputTextboxMenu.setText("Output to Textbox");
740 clustalColour.setText("Clustalx");
742 clustalColour.addActionListener(new java.awt.event.ActionListener()
744 public void actionPerformed(ActionEvent e)
746 clustalColour_actionPerformed(e);
749 zappoColour.setText("Zappo");
750 zappoColour.addActionListener(new java.awt.event.ActionListener()
752 public void actionPerformed(ActionEvent e)
754 zappoColour_actionPerformed(e);
757 taylorColour.setText("Taylor");
758 taylorColour.addActionListener(new java.awt.event.ActionListener()
760 public void actionPerformed(ActionEvent e)
762 taylorColour_actionPerformed(e);
765 hydrophobicityColour.setText("Hydrophobicity");
767 .addActionListener(new java.awt.event.ActionListener()
769 public void actionPerformed(ActionEvent e)
771 hydrophobicityColour_actionPerformed(e);
774 helixColour.setText("Helix Propensity");
775 helixColour.addActionListener(new java.awt.event.ActionListener()
777 public void actionPerformed(ActionEvent e)
779 helixColour_actionPerformed(e);
782 strandColour.setText("Strand Propensity");
783 strandColour.addActionListener(new java.awt.event.ActionListener()
785 public void actionPerformed(ActionEvent e)
787 strandColour_actionPerformed(e);
790 turnColour.setText("Turn Propensity");
791 turnColour.addActionListener(new java.awt.event.ActionListener()
793 public void actionPerformed(ActionEvent e)
795 turnColour_actionPerformed(e);
798 buriedColour.setText("Buried Index");
799 buriedColour.addActionListener(new java.awt.event.ActionListener()
801 public void actionPerformed(ActionEvent e)
803 buriedColour_actionPerformed(e);
806 userDefinedColour.setText("User Defined...");
807 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
809 public void actionPerformed(ActionEvent e)
811 userDefinedColour_actionPerformed(e);
814 PIDColour.setText("Percentage Identity");
815 PIDColour.addActionListener(new java.awt.event.ActionListener()
817 public void actionPerformed(ActionEvent e)
819 PIDColour_actionPerformed(e);
822 BLOSUM62Colour.setText("BLOSUM62 Score");
823 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
825 public void actionPerformed(ActionEvent e)
827 BLOSUM62Colour_actionPerformed(e);
830 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
831 avDistanceTreeBlosumMenuItem
832 .addActionListener(new java.awt.event.ActionListener()
834 public void actionPerformed(ActionEvent e)
836 avTreeBlosumMenuItem_actionPerformed(e);
839 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
841 .addActionListener(new java.awt.event.ActionListener()
843 public void actionPerformed(ActionEvent e)
845 njTreeBlosumMenuItem_actionPerformed(e);
848 annotationPanelMenuItem.setActionCommand("");
849 annotationPanelMenuItem.setText("Show Annotations");
850 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
851 "SHOW_ANNOTATIONS", true));
852 annotationPanelMenuItem
853 .addActionListener(new java.awt.event.ActionListener()
855 public void actionPerformed(ActionEvent e)
857 annotationPanelMenuItem_actionPerformed(e);
860 colourTextMenuItem.setText("Colour Text");
862 .addActionListener(new java.awt.event.ActionListener()
864 public void actionPerformed(ActionEvent e)
866 colourTextMenuItem_actionPerformed(e);
869 htmlMenuItem.setText("HTML");
870 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
872 public void actionPerformed(ActionEvent e)
874 htmlMenuItem_actionPerformed(e);
877 overviewMenuItem.setText("Overview Window");
878 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
880 public void actionPerformed(ActionEvent e)
882 overviewMenuItem_actionPerformed(e);
885 undoMenuItem.setEnabled(false);
886 undoMenuItem.setText("Undo");
887 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
888 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
889 .getMenuShortcutKeyMask(), false));
890 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
892 public void actionPerformed(ActionEvent e)
894 undoMenuItem_actionPerformed(e);
897 redoMenuItem.setEnabled(false);
898 redoMenuItem.setText("Redo");
899 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
900 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
901 .getMenuShortcutKeyMask(), false));
902 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
904 public void actionPerformed(ActionEvent e)
906 redoMenuItem_actionPerformed(e);
909 conservationMenuItem.setText("By Conservation");
911 .addActionListener(new java.awt.event.ActionListener()
913 public void actionPerformed(ActionEvent e)
915 conservationMenuItem_actionPerformed(e);
918 noColourmenuItem.setText("None");
919 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
921 public void actionPerformed(ActionEvent e)
923 noColourmenuItem_actionPerformed(e);
926 wrapMenuItem.setText("Wrap");
927 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
929 public void actionPerformed(ActionEvent e)
931 wrapMenuItem_actionPerformed(e);
934 printMenuItem.setText("Print ...");
935 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
936 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
937 .getMenuShortcutKeyMask(), false));
938 printMenuItem.addActionListener(new java.awt.event.ActionListener()
940 public void actionPerformed(ActionEvent e)
942 printMenuItem_actionPerformed(e);
945 renderGapsMenuItem.setText("Show Gaps");
946 renderGapsMenuItem.setState(true);
948 .addActionListener(new java.awt.event.ActionListener()
950 public void actionPerformed(ActionEvent e)
952 renderGapsMenuItem_actionPerformed(e);
955 findMenuItem.setText("Find...");
956 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
957 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
958 .getMenuShortcutKeyMask(), false));
959 findMenuItem.addActionListener(new java.awt.event.ActionListener()
961 public void actionPerformed(ActionEvent e)
963 findMenuItem_actionPerformed(e);
966 abovePIDThreshold.setText("Above Identity Threshold");
967 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
969 public void actionPerformed(ActionEvent e)
971 abovePIDThreshold_actionPerformed(e);
974 showSeqFeatures.setText("Show Sequence Features");
975 showSeqFeatures.addActionListener(new ActionListener()
977 public void actionPerformed(ActionEvent actionEvent)
979 showSeqFeatures_actionPerformed(actionEvent);
983 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
984 showSeqFeaturesHeight.addActionListener(new ActionListener()
986 public void actionPerformed(ActionEvent actionEvent)
988 showSeqFeaturesHeight_actionPerformed(actionEvent);
991 showDbRefsMenuitem.setText("Show Database Refs");
992 showDbRefsMenuitem.addActionListener(new ActionListener()
995 public void actionPerformed(ActionEvent e)
997 showDbRefs_actionPerformed(e);
1001 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1002 showNpFeatsMenuitem.addActionListener(new ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 showNpFeats_actionPerformed(e);
1011 showGroupConservation.setText("Group Conservation");
1012 showGroupConservation.addActionListener(new ActionListener()
1015 public void actionPerformed(ActionEvent e)
1017 showGroupConservation_actionPerformed(e);
1022 showGroupConsensus.setText("Group Consensus");
1023 showGroupConsensus.addActionListener(new ActionListener()
1026 public void actionPerformed(ActionEvent e)
1028 showGroupConsensus_actionPerformed(e);
1032 showConsensusHistogram.setText("Show Consensus Histogram");
1033 showConsensusHistogram.addActionListener(new ActionListener()
1036 public void actionPerformed(ActionEvent e)
1038 showConsensusHistogram_actionPerformed(e);
1042 showConsensusProfile.setText("Show Consensus Logo");
1043 showConsensusProfile.addActionListener(new ActionListener()
1046 public void actionPerformed(ActionEvent e)
1048 showConsensusProfile_actionPerformed(e);
1052 applyAutoAnnotationSettings.setText("Apply to all groups");
1053 applyAutoAnnotationSettings.setState(false);
1054 applyAutoAnnotationSettings.setVisible(true);
1055 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1058 public void actionPerformed(ActionEvent e)
1060 applyAutoAnnotationSettings_actionPerformed(e);
1065 nucleotideColour.setText("Nucleotide");
1066 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1068 public void actionPerformed(ActionEvent e)
1070 nucleotideColour_actionPerformed(e);
1073 deleteGroups.setText("Undefine groups");
1074 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1075 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1076 .getMenuShortcutKeyMask(), false));
1077 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1079 public void actionPerformed(ActionEvent e)
1081 deleteGroups_actionPerformed(e);
1084 copy.setText("Copy");
1085 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1086 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1087 .getMenuShortcutKeyMask(), false));
1089 copy.addActionListener(new java.awt.event.ActionListener()
1091 public void actionPerformed(ActionEvent e)
1093 copy_actionPerformed(e);
1097 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1098 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1099 .getMenuShortcutKeyMask(), false));
1100 cut.addActionListener(new java.awt.event.ActionListener()
1102 public void actionPerformed(ActionEvent e)
1104 cut_actionPerformed(e);
1107 delete.setText("Delete");
1108 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1109 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1110 delete.addActionListener(new java.awt.event.ActionListener()
1112 public void actionPerformed(ActionEvent e)
1114 delete_actionPerformed(e);
1117 pasteMenu.setText("Paste");
1118 pasteNew.setText("To New Alignment");
1119 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1120 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1121 .getMenuShortcutKeyMask()
1122 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1123 pasteNew.addActionListener(new java.awt.event.ActionListener()
1125 public void actionPerformed(ActionEvent e)
1127 pasteNew_actionPerformed(e);
1130 pasteThis.setText("Add To This Alignment");
1131 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1132 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1133 .getMenuShortcutKeyMask(), false));
1134 pasteThis.addActionListener(new java.awt.event.ActionListener()
1136 public void actionPerformed(ActionEvent e)
1138 pasteThis_actionPerformed(e);
1141 applyToAllGroups.setText("Apply Colour To All Groups");
1142 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1144 public void actionPerformed(ActionEvent e)
1146 applyToAllGroups_actionPerformed(e);
1149 createPNG.addActionListener(new java.awt.event.ActionListener()
1151 public void actionPerformed(ActionEvent e)
1156 createPNG.setActionCommand("Save As PNG Image");
1157 createPNG.setText("PNG");
1158 font.setText("Font...");
1159 font.addActionListener(new java.awt.event.ActionListener()
1161 public void actionPerformed(ActionEvent e)
1163 font_actionPerformed(e);
1167 seqLimits.setText("Show Sequence Limits");
1168 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1169 seqLimits.addActionListener(new java.awt.event.ActionListener()
1171 public void actionPerformed(ActionEvent e)
1173 seqLimit_actionPerformed(e);
1176 epsFile.setText("EPS");
1177 epsFile.addActionListener(new java.awt.event.ActionListener()
1179 public void actionPerformed(ActionEvent e)
1184 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1185 LoadtreeMenuItem.setText("Load Associated Tree");
1186 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 LoadtreeMenuItem_actionPerformed(e);
1193 scaleAbove.setVisible(false);
1194 scaleAbove.setText("Scale Above");
1195 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1197 public void actionPerformed(ActionEvent e)
1199 scaleAbove_actionPerformed(e);
1202 scaleLeft.setVisible(false);
1203 scaleLeft.setSelected(true);
1204 scaleLeft.setText("Scale Left");
1205 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1207 public void actionPerformed(ActionEvent e)
1209 scaleLeft_actionPerformed(e);
1212 scaleRight.setVisible(false);
1213 scaleRight.setSelected(true);
1214 scaleRight.setText("Scale Right");
1215 scaleRight.addActionListener(new java.awt.event.ActionListener()
1217 public void actionPerformed(ActionEvent e)
1219 scaleRight_actionPerformed(e);
1222 centreColumnLabelsMenuItem.setVisible(true);
1223 centreColumnLabelsMenuItem.setState(false);
1224 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1225 centreColumnLabelsMenuItem
1226 .addActionListener(new java.awt.event.ActionListener()
1228 public void actionPerformed(ActionEvent e)
1230 centreColumnLabels_actionPerformed(e);
1233 followHighlightMenuItem.setVisible(true);
1234 followHighlightMenuItem.setState(true);
1235 followHighlightMenuItem.setText("Automatic Scrolling");
1236 followHighlightMenuItem.addActionListener(new ActionListener()
1239 public void actionPerformed(ActionEvent e)
1241 followHighlight_actionPerformed();
1246 modifyPID.setText("Modify Identity Threshold...");
1247 modifyPID.addActionListener(new java.awt.event.ActionListener()
1249 public void actionPerformed(ActionEvent e)
1251 modifyPID_actionPerformed(e);
1254 modifyConservation.setText("Modify Conservation Threshold...");
1256 .addActionListener(new java.awt.event.ActionListener()
1258 public void actionPerformed(ActionEvent e)
1260 modifyConservation_actionPerformed(e);
1263 sortByTreeMenu.setText("By Tree Order");
1264 sort.setText("Sort");
1265 sort.addMenuListener(new MenuListener()
1267 public void menuSelected(MenuEvent e)
1272 public void menuDeselected(MenuEvent e)
1276 public void menuCanceled(MenuEvent e)
1280 sortByAnnotScore.setText("by Score");
1281 sort.add(sortByAnnotScore);
1282 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1285 public void menuCanceled(MenuEvent e)
1289 public void menuDeselected(MenuEvent e)
1293 public void menuSelected(MenuEvent e)
1295 buildSortByAnnotationScoresMenu();
1298 sortByAnnotScore.setVisible(false);
1300 calculateTree.setText("Calculate Tree");
1302 jMenu2.setText("Export Image");
1303 padGapsMenuitem.setText("Pad Gaps");
1304 padGapsMenuitem.setState(jalview.bin.Cache
1305 .getDefault("PAD_GAPS", false));
1306 padGapsMenuitem.addActionListener(new ActionListener()
1308 public void actionPerformed(ActionEvent e)
1310 padGapsMenuitem_actionPerformed(e);
1313 vamsasStore.setVisible(false);
1314 vamsasStore.setText("VAMSAS store");
1315 vamsasStore.addActionListener(new ActionListener()
1317 public void actionPerformed(ActionEvent e)
1319 vamsasStore_actionPerformed(e);
1322 showTranslation.setText("Translate cDNA");
1323 showTranslation.addActionListener(new ActionListener()
1325 public void actionPerformed(ActionEvent e)
1327 showTranslation_actionPerformed(e);
1330 extractScores.setText("Extract Scores...");
1331 extractScores.addActionListener(new ActionListener()
1333 public void actionPerformed(ActionEvent e)
1335 extractScores_actionPerformed(e);
1338 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1340 showProducts.setText("Get Cross References");
1342 * showProducts.addActionListener(new ActionListener() {
1344 * public void actionPerformed(ActionEvent e) {
1345 * showProducts_actionPerformed(e); } });
1347 featureSettings.setText("Feature Settings...");
1348 featureSettings.addActionListener(new ActionListener()
1350 public void actionPerformed(ActionEvent e)
1352 featureSettings_actionPerformed(e);
1355 fetchSequence.setText("Fetch Sequence(s)...");
1356 fetchSequence.addActionListener(new ActionListener()
1358 public void actionPerformed(ActionEvent e)
1360 fetchSequence_actionPerformed(e);
1364 annotationColour.setText("By Annotation...");
1365 annotationColour.addActionListener(new ActionListener()
1367 public void actionPerformed(ActionEvent e)
1369 annotationColour_actionPerformed(e);
1372 associatedData.setText("Load Features / Annotations");
1373 associatedData.addActionListener(new ActionListener()
1375 public void actionPerformed(ActionEvent e)
1377 associatedData_actionPerformed(e);
1380 autoCalculate.setText("Autocalculate Consensus");
1381 autoCalculate.setState(jalview.bin.Cache.getDefault(
1382 "AUTO_CALC_CONSENSUS", true));
1383 autoCalculate.addActionListener(new ActionListener()
1385 public void actionPerformed(ActionEvent e)
1387 autoCalculate_actionPerformed(e);
1390 addSequenceMenu.setText("Add Sequences");
1391 addFromFile.setText("From File");
1392 addFromFile.addActionListener(new ActionListener()
1394 public void actionPerformed(ActionEvent e)
1396 addFromFile_actionPerformed(e);
1399 addFromText.setText("From Textbox");
1400 addFromText.addActionListener(new ActionListener()
1402 public void actionPerformed(ActionEvent e)
1404 addFromText_actionPerformed(e);
1407 addFromURL.setText("From URL");
1408 addFromURL.addActionListener(new ActionListener()
1410 public void actionPerformed(ActionEvent e)
1412 addFromURL_actionPerformed(e);
1415 exportFeatures.setText("Export Features...");
1416 exportFeatures.addActionListener(new ActionListener()
1418 public void actionPerformed(ActionEvent e)
1420 exportFeatures_actionPerformed(e);
1423 exportAnnotations.setText("Export Annotations...");
1424 exportAnnotations.addActionListener(new ActionListener()
1426 public void actionPerformed(ActionEvent e)
1428 exportAnnotations_actionPerformed(e);
1431 statusPanel.setLayout(gridLayout1);
1432 jMenu3.setText("Show");
1433 showAllSeqs.setText("All Sequences");
1434 showAllSeqs.addActionListener(new ActionListener()
1436 public void actionPerformed(ActionEvent e)
1438 showAllSeqs_actionPerformed(e);
1441 showAllColumns.setText("All Columns");
1442 showAllColumns.addActionListener(new ActionListener()
1444 public void actionPerformed(ActionEvent e)
1446 showAllColumns_actionPerformed(e);
1449 hideMenu.setText("Hide");
1450 hideSelSequences.setText("Selected Sequences");
1451 hideSelSequences.addActionListener(new ActionListener()
1453 public void actionPerformed(ActionEvent e)
1455 hideSelSequences_actionPerformed(e);
1458 hideSelColumns.setText("Selected Columns");
1459 hideSelColumns.addActionListener(new ActionListener()
1461 public void actionPerformed(ActionEvent e)
1463 hideSelColumns_actionPerformed(e);
1466 hiddenMarkers.setText("Show Hidden Markers");
1467 hiddenMarkers.addActionListener(new ActionListener()
1469 public void actionPerformed(ActionEvent e)
1471 hiddenMarkers_actionPerformed(e);
1474 invertColSel.setText("Invert Column Selection");
1475 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1476 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1477 .getMenuShortcutKeyMask()
1478 | java.awt.event.KeyEvent.ALT_MASK, false));
1479 invertColSel.addActionListener(new ActionListener()
1481 public void actionPerformed(ActionEvent e)
1483 invertColSel_actionPerformed(e);
1486 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1488 public void stateChanged(ChangeEvent evt)
1490 JTabbedPane pane = (JTabbedPane) evt.getSource();
1491 int sel = pane.getSelectedIndex();
1492 tabSelectionChanged(sel);
1495 tabbedPane.addMouseListener(new MouseAdapter()
1497 public void mousePressed(MouseEvent e)
1499 tabbedPane_mousePressed(e);
1502 tabbedPane.addFocusListener(new FocusAdapter()
1504 public void focusGained(FocusEvent e)
1506 tabbedPane_focusGained(e);
1509 save.setText("Save");
1510 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1511 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1512 .getMenuShortcutKeyMask(), false));
1513 save.addActionListener(new ActionListener()
1515 public void actionPerformed(ActionEvent e)
1517 save_actionPerformed(e);
1520 reload.setEnabled(false);
1521 reload.setText("Reload");
1522 reload.addActionListener(new ActionListener()
1524 public void actionPerformed(ActionEvent e)
1526 reload_actionPerformed(e);
1529 newView.setText("New View");
1530 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1531 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1532 .getMenuShortcutKeyMask(), false));
1533 newView.addActionListener(new ActionListener()
1535 public void actionPerformed(ActionEvent e)
1537 newView_actionPerformed(e);
1540 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1541 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1542 textColour.setText("Colour Text ...");
1543 textColour.addActionListener(new ActionListener()
1545 public void actionPerformed(ActionEvent e)
1547 textColour_actionPerformed(e);
1550 formatMenu.setText("Format");
1551 selectMenu.setText("Select");
1552 idRightAlign.setText("Right Align Sequence Id");
1553 idRightAlign.addActionListener(new ActionListener()
1555 public void actionPerformed(ActionEvent e)
1557 idRightAlign_actionPerformed(e);
1560 gatherViews.setEnabled(false);
1561 gatherViews.setText("Gather Views");
1562 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1563 java.awt.event.KeyEvent.VK_G, 0, false));
1564 gatherViews.addActionListener(new ActionListener()
1566 public void actionPerformed(ActionEvent e)
1568 gatherViews_actionPerformed(e);
1571 expandViews.setEnabled(false);
1572 expandViews.setText("Expand Views");
1573 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1574 java.awt.event.KeyEvent.VK_X, 0, false));
1575 expandViews.addActionListener(new ActionListener()
1577 public void actionPerformed(ActionEvent e)
1579 expandViews_actionPerformed(e);
1582 pageSetup.setText("Page Setup ...");
1583 pageSetup.addActionListener(new ActionListener()
1585 public void actionPerformed(ActionEvent e)
1587 pageSetup_actionPerformed(e);
1590 alignmentProperties.setText("Alignment Properties...");
1591 alignmentProperties.addActionListener(new ActionListener()
1593 public void actionPerformed(ActionEvent actionEvent)
1595 alignmentProperties();
1598 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1599 autoAnnMenu.setText("Autocalculated Annotation");
1600 alignFrameMenuBar.add(fileMenu);
1601 alignFrameMenuBar.add(editMenu);
1602 alignFrameMenuBar.add(selectMenu);
1603 alignFrameMenuBar.add(viewMenu);
1604 alignFrameMenuBar.add(formatMenu);
1605 alignFrameMenuBar.add(colourMenu);
1606 alignFrameMenuBar.add(calculateMenu);
1607 alignFrameMenuBar.add(webService);
1608 fileMenu.add(fetchSequence);
1609 fileMenu.add(addSequenceMenu);
1610 fileMenu.add(reload);
1611 fileMenu.addSeparator();
1612 fileMenu.add(vamsasStore);
1614 fileMenu.add(saveAs);
1615 fileMenu.add(outputTextboxMenu);
1616 fileMenu.add(pageSetup);
1617 fileMenu.add(printMenuItem);
1618 fileMenu.addSeparator();
1619 fileMenu.add(jMenu2);
1620 fileMenu.add(exportFeatures);
1621 fileMenu.add(exportAnnotations);
1622 fileMenu.add(LoadtreeMenuItem);
1623 fileMenu.add(associatedData);
1624 fileMenu.addSeparator();
1625 fileMenu.add(closeMenuItem);
1626 editMenu.add(undoMenuItem);
1627 editMenu.add(redoMenuItem);
1630 editMenu.add(pasteMenu);
1631 editMenu.add(delete);
1632 editMenu.addSeparator();
1633 editMenu.add(remove2LeftMenuItem);
1634 editMenu.add(remove2RightMenuItem);
1635 editMenu.add(removeGappedColumnMenuItem);
1636 editMenu.add(removeAllGapsMenuItem);
1637 editMenu.add(removeRedundancyMenuItem);
1638 editMenu.addSeparator();
1639 // dont add these yet in the CVS build - they cannot be undone!
1640 editMenu.add(justifyLeftMenuItem);
1641 editMenu.add(justifyRightMenuItem);
1642 editMenu.addSeparator();
1643 editMenu.add(padGapsMenuitem);
1644 viewMenu.add(newView);
1645 viewMenu.add(expandViews);
1646 viewMenu.add(gatherViews);
1647 viewMenu.addSeparator();
1648 viewMenu.add(jMenu3);
1649 viewMenu.add(hideMenu);
1650 viewMenu.addSeparator();
1651 viewMenu.add(followHighlightMenuItem);
1652 viewMenu.add(annotationPanelMenuItem);
1653 autoAnnMenu.add(applyAutoAnnotationSettings);
1654 autoAnnMenu.add(showConsensusHistogram);
1655 autoAnnMenu.add(showConsensusProfile);
1656 autoAnnMenu.addSeparator();
1657 autoAnnMenu.add(showGroupConservation);
1658 autoAnnMenu.add(showGroupConsensus);
1659 viewMenu.add(autoAnnMenu);
1660 viewMenu.addSeparator();
1661 viewMenu.add(showSeqFeatures);
1662 //viewMenu.add(showSeqFeaturesHeight);
1664 viewMenu.add(featureSettings);
1665 tooltipSettingsMenu.add(showDbRefsMenuitem);
1666 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1667 viewMenu.add(tooltipSettingsMenu);
1668 viewMenu.addSeparator();
1669 viewMenu.add(alignmentProperties);
1670 viewMenu.addSeparator();
1671 viewMenu.add(overviewMenuItem);
1672 colourMenu.add(applyToAllGroups);
1673 colourMenu.add(textColour);
1674 colourMenu.addSeparator();
1675 colourMenu.add(noColourmenuItem);
1676 colourMenu.add(clustalColour);
1677 colourMenu.add(BLOSUM62Colour);
1678 colourMenu.add(PIDColour);
1679 colourMenu.add(zappoColour);
1680 colourMenu.add(taylorColour);
1681 colourMenu.add(hydrophobicityColour);
1682 colourMenu.add(helixColour);
1683 colourMenu.add(strandColour);
1684 colourMenu.add(turnColour);
1685 colourMenu.add(buriedColour);
1686 colourMenu.add(nucleotideColour);
1687 colourMenu.add(userDefinedColour);
1688 colourMenu.addSeparator();
1689 colourMenu.add(conservationMenuItem);
1690 colourMenu.add(modifyConservation);
1691 colourMenu.add(abovePIDThreshold);
1692 colourMenu.add(modifyPID);
1693 colourMenu.add(annotationColour);
1694 calculateMenu.add(sort);
1695 calculateMenu.add(calculateTree);
1696 calculateMenu.addSeparator();
1697 calculateMenu.add(pairwiseAlignmentMenuItem);
1698 calculateMenu.add(PCAMenuItem);
1699 calculateMenu.addSeparator();
1700 calculateMenu.add(showTranslation);
1701 calculateMenu.add(showProducts);
1702 calculateMenu.add(autoCalculate);
1703 calculateMenu.addSeparator();
1704 calculateMenu.add(extractScores);
1705 webServiceNoServices = new JMenuItem("<No Services>");
1706 webService.add(webServiceNoServices);
1707 pasteMenu.add(pasteNew);
1708 pasteMenu.add(pasteThis);
1709 sort.add(sortIDMenuItem);
1710 sort.add(sortLengthMenuItem);
1711 sort.add(sortGroupMenuItem);
1712 sort.add(sortPairwiseMenuItem);
1713 sort.add(sortByTreeMenu);
1714 calculateTree.add(averageDistanceTreeMenuItem);
1715 calculateTree.add(neighbourTreeMenuItem);
1716 calculateTree.add(avDistanceTreeBlosumMenuItem);
1717 calculateTree.add(njTreeBlosumMenuItem);
1718 jMenu2.add(htmlMenuItem);
1719 jMenu2.add(epsFile);
1720 jMenu2.add(createPNG);
1721 addSequenceMenu.add(addFromFile);
1722 addSequenceMenu.add(addFromText);
1723 addSequenceMenu.add(addFromURL);
1724 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1725 statusPanel.add(statusBar, null);
1726 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1727 jMenu3.add(showAllColumns);
1728 jMenu3.add(showAllSeqs);
1729 hideMenu.add(hideSelColumns);
1730 hideMenu.add(hideSelSequences);
1731 formatMenu.add(font);
1732 formatMenu.addSeparator();
1733 formatMenu.add(wrapMenuItem);
1734 formatMenu.add(scaleAbove);
1735 formatMenu.add(scaleLeft);
1736 formatMenu.add(scaleRight);
1737 formatMenu.add(seqLimits);
1738 formatMenu.add(idRightAlign);
1739 formatMenu.add(hiddenMarkers);
1740 formatMenu.add(viewBoxesMenuItem);
1741 formatMenu.add(viewTextMenuItem);
1742 formatMenu.add(colourTextMenuItem);
1743 formatMenu.add(renderGapsMenuItem);
1744 formatMenu.add(centreColumnLabelsMenuItem);
1745 formatMenu.add(showUnconservedMenuItem);
1746 selectMenu.add(findMenuItem);
1747 selectMenu.addSeparator();
1748 selectMenu.add(selectAllSequenceMenuItem);
1749 selectMenu.add(deselectAllSequenceMenuItem);
1750 selectMenu.add(invertSequenceMenuItem);
1751 selectMenu.add(invertColSel);
1752 selectMenu.add(deleteGroups);
1753 selectMenu.add(grpsFromSelection);
1756 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1758 // TODO Auto-generated method stub
1762 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1764 // TODO Auto-generated method stub
1768 protected void showConsensusProfile_actionPerformed(ActionEvent e)
1770 // TODO Auto-generated method stub
1774 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1776 // TODO Auto-generated method stub
1780 protected void showGroupConsensus_actionPerformed(ActionEvent e)
1782 // TODO Auto-generated method stub
1786 protected void showGroupConservation_actionPerformed(ActionEvent e)
1788 // TODO Auto-generated method stub
1792 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1794 // TODO Auto-generated method stub
1798 protected void showSeqFeaturesHeight_actionPerformed(
1799 ActionEvent actionEvent)
1801 // TODO Auto-generated method stub
1805 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1807 // TODO Auto-generated method stub
1811 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1813 // TODO Auto-generated method stub
1817 protected void followHighlight_actionPerformed()
1819 // TODO Auto-generated method stub
1823 protected void showNpFeats_actionPerformed(ActionEvent e)
1825 // TODO Auto-generated method stub
1829 protected void showDbRefs_actionPerformed(ActionEvent e)
1831 // TODO Auto-generated method stub
1835 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1839 protected void showProducts_actionPerformed(ActionEvent e)
1843 protected void buildSortByAnnotationScoresMenu()
1847 protected void extractScores_actionPerformed(ActionEvent e)
1851 protected void outputText_actionPerformed(ActionEvent e)
1855 public void addFromFile_actionPerformed(ActionEvent e)
1860 public void addFromText_actionPerformed(ActionEvent e)
1865 public void addFromURL_actionPerformed(ActionEvent e)
1870 public void exportFeatures_actionPerformed(ActionEvent e)
1875 public void exportAnnotations_actionPerformed(ActionEvent e)
1880 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1884 protected void closeMenuItem_actionPerformed(boolean b)
1888 protected void redoMenuItem_actionPerformed(ActionEvent e)
1892 protected void undoMenuItem_actionPerformed(ActionEvent e)
1896 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1900 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1904 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1908 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1912 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1916 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1920 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1924 protected void wrapMenuItem_actionPerformed(ActionEvent e)
1928 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1932 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1936 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1940 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1944 protected void overviewMenuItem_actionPerformed(ActionEvent e)
1948 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1952 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1956 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
1960 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1964 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1968 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1972 protected void PCAMenuItem_actionPerformed(ActionEvent e)
1976 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1980 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1984 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1988 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1992 protected void clustalColour_actionPerformed(ActionEvent e)
1996 protected void zappoColour_actionPerformed(ActionEvent e)
2000 protected void taylorColour_actionPerformed(ActionEvent e)
2004 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2008 protected void helixColour_actionPerformed(ActionEvent e)
2012 protected void strandColour_actionPerformed(ActionEvent e)
2016 protected void turnColour_actionPerformed(ActionEvent e)
2020 protected void buriedColour_actionPerformed(ActionEvent e)
2024 protected void userDefinedColour_actionPerformed(ActionEvent e)
2028 protected void PIDColour_actionPerformed(ActionEvent e)
2032 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2036 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2040 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2044 protected void printMenuItem_actionPerformed(ActionEvent e)
2048 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2052 protected void findMenuItem_actionPerformed(ActionEvent e)
2056 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2060 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2064 protected void nucleotideColour_actionPerformed(ActionEvent e)
2068 protected void deleteGroups_actionPerformed(ActionEvent e)
2072 protected void copy_actionPerformed(ActionEvent e)
2076 protected void cut_actionPerformed(ActionEvent e)
2080 protected void delete_actionPerformed(ActionEvent e)
2084 protected void pasteNew_actionPerformed(ActionEvent e)
2088 protected void pasteThis_actionPerformed(ActionEvent e)
2092 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2096 public void createPNG(java.io.File f)
2100 protected void font_actionPerformed(ActionEvent e)
2104 protected void seqLimit_actionPerformed(ActionEvent e)
2108 public void seqDBRef_actionPerformed(ActionEvent e)
2113 public void createEPS(java.io.File f)
2117 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2121 protected void jpred_actionPerformed(ActionEvent e)
2125 protected void scaleAbove_actionPerformed(ActionEvent e)
2129 protected void scaleLeft_actionPerformed(ActionEvent e)
2133 protected void scaleRight_actionPerformed(ActionEvent e)
2137 protected void modifyPID_actionPerformed(ActionEvent e)
2141 protected void modifyConservation_actionPerformed(ActionEvent e)
2145 protected void saveAs_actionPerformed(ActionEvent e)
2149 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2153 public void vamsasStore_actionPerformed(ActionEvent e)
2158 public void vamsasLoad_actionPerformed(ActionEvent e)
2163 public void showTranslation_actionPerformed(ActionEvent e)
2168 public void featureSettings_actionPerformed(ActionEvent e)
2173 public void fetchSequence_actionPerformed(ActionEvent e)
2178 public void smoothFont_actionPerformed(ActionEvent e)
2183 public void annotationColour_actionPerformed(ActionEvent e)
2188 public void associatedData_actionPerformed(ActionEvent e)
2193 public void autoCalculate_actionPerformed(ActionEvent e)
2198 public void showAllSeqs_actionPerformed(ActionEvent e)
2203 public void showAllColumns_actionPerformed(ActionEvent e)
2208 public void hideSelSequences_actionPerformed(ActionEvent e)
2213 public void hideSelColumns_actionPerformed(ActionEvent e)
2218 public void hiddenMarkers_actionPerformed(ActionEvent e)
2223 public void findPdbId_actionPerformed(ActionEvent e)
2228 public void enterPdbId_actionPerformed(ActionEvent e)
2233 public void pdbFile_actionPerformed(ActionEvent e)
2238 public void invertColSel_actionPerformed(ActionEvent e)
2243 public void tabSelectionChanged(int sel)
2248 public void tabbedPane_mousePressed(MouseEvent e)
2253 public void tabbedPane_focusGained(FocusEvent e)
2258 public void save_actionPerformed(ActionEvent e)
2263 public void reload_actionPerformed(ActionEvent e)
2268 public void newView_actionPerformed(ActionEvent e)
2273 public void textColour_actionPerformed(ActionEvent e)
2278 public void idRightAlign_actionPerformed(ActionEvent e)
2283 public void expandViews_actionPerformed(ActionEvent e)
2288 public void gatherViews_actionPerformed(ActionEvent e)
2293 public void buildTreeMenu()
2298 public void pageSetup_actionPerformed(ActionEvent e)
2303 public void alignmentProperties()