2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.jbgui;
21 import java.awt.event.*;
24 import javax.swing.event.*;
26 import jalview.schemes.*;
28 public class GAlignFrame extends JInternalFrame
30 protected JMenuBar alignFrameMenuBar = new JMenuBar();
32 protected JMenu fileMenu = new JMenu();
34 protected JMenuItem closeMenuItem = new JMenuItem();
36 protected JMenu editMenu = new JMenu();
38 protected JMenu viewMenu = new JMenu();
40 protected JMenu colourMenu = new JMenu();
42 protected JMenu calculateMenu = new JMenu();
44 protected JMenu webService = new JMenu();
46 protected JMenuItem webServiceNoServices;
48 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
50 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
52 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
54 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
56 protected JMenuItem remove2RightMenuItem = new JMenuItem();
58 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
60 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
62 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
64 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
66 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
68 protected JMenuItem sortIDMenuItem = new JMenuItem();
70 protected JMenuItem sortLengthMenuItem = new JMenuItem();
72 protected JMenuItem sortGroupMenuItem = new JMenuItem();
74 protected JMenu sortByAnnotScore = new JMenu();
76 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
78 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
80 protected JMenuItem PCAMenuItem = new JMenuItem();
82 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
84 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
86 BorderLayout borderLayout1 = new BorderLayout();
88 public JLabel statusBar = new JLabel();
90 protected JMenuItem saveAs = new JMenuItem();
92 protected JMenu outputTextboxMenu = new JMenu();
94 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
96 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
98 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
100 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
102 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
104 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
106 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
108 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
110 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
112 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
114 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
116 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
118 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
120 // protected JRadioButtonMenuItem covariationColour = new
121 // JRadioButtonMenuItem();
123 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
125 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
127 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
129 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
131 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
133 JMenuItem htmlMenuItem = new JMenuItem();
135 JMenuItem overviewMenuItem = new JMenuItem();
137 protected JMenuItem undoMenuItem = new JMenuItem();
139 protected JMenuItem redoMenuItem = new JMenuItem();
141 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
143 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
145 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
147 JMenuItem printMenuItem = new JMenuItem();
149 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
151 JMenuItem findMenuItem = new JMenuItem();
153 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
155 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
157 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
159 JMenuItem deleteGroups = new JMenuItem();
161 JMenuItem delete = new JMenuItem();
163 JMenuItem copy = new JMenuItem();
165 JMenuItem cut = new JMenuItem();
167 JMenu pasteMenu = new JMenu();
169 JMenuItem pasteNew = new JMenuItem();
171 JMenuItem pasteThis = new JMenuItem();
173 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
175 JMenuItem createPNG = new JMenuItem();
177 protected JMenuItem font = new JMenuItem();
179 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
181 JMenuItem epsFile = new JMenuItem();
183 JMenuItem LoadtreeMenuItem = new JMenuItem();
185 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
187 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
189 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
191 protected JMenuItem modifyPID = new JMenuItem();
193 protected JMenuItem modifyConservation = new JMenuItem();
195 protected JMenu sortByTreeMenu = new JMenu();
197 protected JMenu sort = new JMenu();
199 protected JMenu calculateTree = new JMenu();
201 JMenu jMenu2 = new JMenu();
203 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
205 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
207 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
209 protected ButtonGroup colours = new ButtonGroup();
211 JMenuItem vamsasStore = new JMenuItem();
213 protected JMenuItem showTranslation = new JMenuItem();
215 protected JMenuItem extractScores = new JMenuItem();
217 protected JMenu showProducts = new JMenu();
219 public JMenuItem featureSettings = new JMenuItem();
221 JMenuItem fetchSequence = new JMenuItem();
223 JMenuItem annotationColour = new JMenuItem();
225 JMenuItem rnahelicesColour = new JMenuItem();
227 JMenuItem associatedData = new JMenuItem();
229 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
231 JMenu addSequenceMenu = new JMenu();
233 JMenuItem addFromFile = new JMenuItem();
235 JMenuItem addFromText = new JMenuItem();
237 JMenuItem addFromURL = new JMenuItem();
239 JMenuItem exportAnnotations = new JMenuItem();
241 JMenuItem exportFeatures = new JMenuItem();
243 protected JPanel statusPanel = new JPanel();
245 GridLayout gridLayout1 = new GridLayout();
247 JMenu jMenu3 = new JMenu();
249 JMenuItem showAllSeqs = new JMenuItem();
251 JMenuItem showAllColumns = new JMenuItem();
253 JMenu hideMenu = new JMenu();
255 JMenuItem hideSelSequences = new JMenuItem();
257 JMenuItem hideSelColumns = new JMenuItem();
259 JMenuItem hideAllButSelection = new JMenuItem();
261 JMenuItem hideAllSelection = new JMenuItem();
263 JMenuItem showAllhidden = new JMenuItem();
265 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
267 JMenuItem invertColSel = new JMenuItem();
269 protected JTabbedPane tabbedPane = new JTabbedPane();
271 JMenuItem save = new JMenuItem();
273 protected JMenuItem reload = new JMenuItem();
275 JMenuItem newView = new JMenuItem();
277 JMenuItem textColour = new JMenuItem();
279 JMenu formatMenu = new JMenu();
281 JMenu selectMenu = new JMenu();
283 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
285 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
287 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
289 protected JMenuItem gatherViews = new JMenuItem();
291 protected JMenuItem expandViews = new JMenuItem();
293 JMenuItem pageSetup = new JMenuItem();
295 JMenuItem alignmentProperties = new JMenuItem();
297 JMenu tooltipSettingsMenu = new JMenu();
299 private JMenuItem justifyLeftMenuItem = new JMenuItem();
301 private JMenuItem justifyRightMenuItem = new JMenuItem();
303 JMenu autoAnnMenu = new JMenu();
305 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
307 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
309 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
311 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
313 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
315 private JMenuItem grpsFromSelection = new JMenuItem();
322 setJMenuBar(alignFrameMenuBar);
324 // dynamically fill save as menu with available formats
325 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
327 JMenuItem item = new JMenuItem(
328 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
330 item.addActionListener(new java.awt.event.ActionListener()
332 public void actionPerformed(ActionEvent e)
334 outputText_actionPerformed(e);
338 outputTextboxMenu.add(item);
340 } catch (Exception e)
344 if (!new jalview.util.Platform().isAMac())
346 closeMenuItem.setMnemonic('C');
347 outputTextboxMenu.setMnemonic('T');
348 undoMenuItem.setMnemonic('Z');
349 redoMenuItem.setMnemonic('0');
350 copy.setMnemonic('C');
351 cut.setMnemonic('U');
352 pasteMenu.setMnemonic('P');
353 reload.setMnemonic('R');
356 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
358 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
359 .getUserColourSchemes().keys();
361 while (userColours.hasMoreElements())
363 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
364 userColours.nextElement().toString());
365 radioItem.setName("USER_DEFINED");
366 radioItem.addMouseListener(new MouseAdapter()
368 public void mousePressed(MouseEvent evt)
370 if (evt.isControlDown()
371 || SwingUtilities.isRightMouseButton(evt))
373 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
375 int option = JOptionPane.showInternalConfirmDialog(
376 jalview.gui.Desktop.desktop,
377 "Remove from default list?",
378 "Remove user defined colour",
379 JOptionPane.YES_NO_OPTION);
380 if (option == JOptionPane.YES_OPTION)
382 jalview.gui.UserDefinedColours
383 .removeColourFromDefaults(radioItem.getText());
384 colourMenu.remove(radioItem);
388 radioItem.addActionListener(new ActionListener()
390 public void actionPerformed(ActionEvent evt)
392 userDefinedColour_actionPerformed(evt);
399 radioItem.addActionListener(new ActionListener()
401 public void actionPerformed(ActionEvent evt)
403 userDefinedColour_actionPerformed(evt);
406 colourMenu.insert(radioItem, 15);
407 colours.add(radioItem);
410 colours.add(noColourmenuItem);
411 colours.add(clustalColour);
412 colours.add(zappoColour);
413 colours.add(taylorColour);
414 colours.add(hydrophobicityColour);
415 colours.add(helixColour);
416 colours.add(strandColour);
417 colours.add(turnColour);
418 colours.add(buriedColour);
419 colours.add(userDefinedColour);
420 colours.add(PIDColour);
421 colours.add(BLOSUM62Colour);
422 colours.add(nucleotideColour);
423 colours.add(purinePyrimidineColour);
424 // colours.add(covariationColour);
426 setColourSelected(jalview.bin.Cache
427 .getDefault("DEFAULT_COLOUR", "None"));
431 public void setColourSelected(String defaultColour)
434 if (defaultColour != null)
436 int index = ColourSchemeProperty
437 .getColourIndexFromName(defaultColour);
441 case ColourSchemeProperty.CLUSTAL:
442 clustalColour.setSelected(true);
446 case ColourSchemeProperty.BLOSUM:
447 BLOSUM62Colour.setSelected(true);
451 case ColourSchemeProperty.PID:
452 PIDColour.setSelected(true);
456 case ColourSchemeProperty.ZAPPO:
457 zappoColour.setSelected(true);
461 case ColourSchemeProperty.TAYLOR:
462 taylorColour.setSelected(true);
465 case ColourSchemeProperty.HYDROPHOBIC:
466 hydrophobicityColour.setSelected(true);
470 case ColourSchemeProperty.HELIX:
471 helixColour.setSelected(true);
475 case ColourSchemeProperty.STRAND:
476 strandColour.setSelected(true);
480 case ColourSchemeProperty.TURN:
481 turnColour.setSelected(true);
485 case ColourSchemeProperty.BURIED:
486 buriedColour.setSelected(true);
490 case ColourSchemeProperty.NUCLEOTIDE:
491 nucleotideColour.setSelected(true);
495 case ColourSchemeProperty.PURINEPYRIMIDINE:
496 purinePyrimidineColour.setSelected(true);
500 * case ColourSchemeProperty.COVARIATION:
501 * covariationColour.setSelected(true);
505 case ColourSchemeProperty.USER_DEFINED:
506 userDefinedColour.setSelected(true);
509 case ColourSchemeProperty.NONE:
511 noColourmenuItem.setSelected(true);
519 private void jbInit() throws Exception
521 fileMenu.setText("File");
522 saveAs.setText("Save As...");
523 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
524 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
525 .getMenuShortcutKeyMask()
526 | java.awt.event.KeyEvent.SHIFT_MASK, false));
527 saveAs.addActionListener(new ActionListener()
529 public void actionPerformed(ActionEvent e)
531 saveAs_actionPerformed(e);
534 closeMenuItem.setText("Close");
535 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
536 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
537 .getMenuShortcutKeyMask(), false));
538 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
540 public void actionPerformed(ActionEvent e)
542 closeMenuItem_actionPerformed(false);
545 editMenu.setText("Edit");
546 viewMenu.setText("View");
547 colourMenu.setText("Colour");
548 calculateMenu.setText("Calculate");
549 webService.setText("Web Service");
550 selectAllSequenceMenuItem.setText("Select All");
551 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
552 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
553 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
554 selectAllSequenceMenuItem
555 .addActionListener(new java.awt.event.ActionListener()
557 public void actionPerformed(ActionEvent e)
559 selectAllSequenceMenuItem_actionPerformed(e);
562 deselectAllSequenceMenuItem.setText("Deselect All");
563 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
564 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
565 deselectAllSequenceMenuItem
566 .addActionListener(new java.awt.event.ActionListener()
568 public void actionPerformed(ActionEvent e)
570 deselectAllSequenceMenuItem_actionPerformed(e);
573 invertSequenceMenuItem.setText("Invert Sequence Selection");
574 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
575 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
576 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
577 invertSequenceMenuItem
578 .addActionListener(new java.awt.event.ActionListener()
580 public void actionPerformed(ActionEvent e)
582 invertSequenceMenuItem_actionPerformed(e);
585 grpsFromSelection.setText("Make Groups for selection");
586 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
588 public void actionPerformed(ActionEvent e)
590 makeGrpsFromSelection_actionPerformed(e);
594 remove2LeftMenuItem.setText("Remove Left");
595 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
596 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
597 .getMenuShortcutKeyMask(), false));
599 .addActionListener(new java.awt.event.ActionListener()
601 public void actionPerformed(ActionEvent e)
603 remove2LeftMenuItem_actionPerformed(e);
606 remove2RightMenuItem.setText("Remove Right");
607 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
608 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
609 .getMenuShortcutKeyMask(), false));
611 .addActionListener(new java.awt.event.ActionListener()
613 public void actionPerformed(ActionEvent e)
615 remove2RightMenuItem_actionPerformed(e);
618 removeGappedColumnMenuItem.setText("Remove Empty Columns");
619 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
620 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
621 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
622 removeGappedColumnMenuItem
623 .addActionListener(new java.awt.event.ActionListener()
625 public void actionPerformed(ActionEvent e)
627 removeGappedColumnMenuItem_actionPerformed(e);
630 removeAllGapsMenuItem.setText("Remove All Gaps");
631 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
632 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
633 .getDefaultToolkit().getMenuShortcutKeyMask()
634 | java.awt.event.KeyEvent.SHIFT_MASK, false));
635 removeAllGapsMenuItem
636 .addActionListener(new java.awt.event.ActionListener()
638 public void actionPerformed(ActionEvent e)
640 removeAllGapsMenuItem_actionPerformed(e);
643 justifyLeftMenuItem.setText("Left Justify Alignment");
645 .addActionListener(new java.awt.event.ActionListener()
647 public void actionPerformed(ActionEvent e)
649 justifyLeftMenuItem_actionPerformed(e);
652 justifyRightMenuItem.setText("Right Justify Alignment");
654 .addActionListener(new java.awt.event.ActionListener()
656 public void actionPerformed(ActionEvent e)
658 justifyRightMenuItem_actionPerformed(e);
661 viewBoxesMenuItem.setText("Boxes");
662 viewBoxesMenuItem.setState(true);
663 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
665 public void actionPerformed(ActionEvent e)
667 viewBoxesMenuItem_actionPerformed(e);
670 viewTextMenuItem.setText("Text");
671 viewTextMenuItem.setState(true);
672 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
674 public void actionPerformed(ActionEvent e)
676 viewTextMenuItem_actionPerformed(e);
679 showNonconservedMenuItem.setText("Show nonconserved");
680 showNonconservedMenuItem.setState(false);
681 showNonconservedMenuItem
682 .addActionListener(new java.awt.event.ActionListener()
684 public void actionPerformed(ActionEvent e)
686 showUnconservedMenuItem_actionPerformed(e);
689 sortPairwiseMenuItem.setText("by Pairwise Identity");
691 .addActionListener(new java.awt.event.ActionListener()
693 public void actionPerformed(ActionEvent e)
695 sortPairwiseMenuItem_actionPerformed(e);
698 sortIDMenuItem.setText("by ID");
699 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
701 public void actionPerformed(ActionEvent e)
703 sortIDMenuItem_actionPerformed(e);
706 sortLengthMenuItem.setText("By Length");
708 .addActionListener(new java.awt.event.ActionListener()
710 public void actionPerformed(ActionEvent e)
712 sortLengthMenuItem_actionPerformed(e);
715 sortGroupMenuItem.setText("by Group");
716 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
718 public void actionPerformed(ActionEvent e)
720 sortGroupMenuItem_actionPerformed(e);
723 removeRedundancyMenuItem.setText("Remove Redundancy...");
724 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
725 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
726 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
727 removeRedundancyMenuItem
728 .addActionListener(new java.awt.event.ActionListener()
730 public void actionPerformed(ActionEvent e)
732 removeRedundancyMenuItem_actionPerformed(e);
735 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
736 pairwiseAlignmentMenuItem
737 .addActionListener(new java.awt.event.ActionListener()
739 public void actionPerformed(ActionEvent e)
741 pairwiseAlignmentMenuItem_actionPerformed(e);
744 PCAMenuItem.setText("Principal Component Analysis");
745 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
747 public void actionPerformed(ActionEvent e)
749 PCAMenuItem_actionPerformed(e);
752 averageDistanceTreeMenuItem
753 .setText("Average Distance Using % Identity");
754 averageDistanceTreeMenuItem
755 .addActionListener(new java.awt.event.ActionListener()
757 public void actionPerformed(ActionEvent e)
759 averageDistanceTreeMenuItem_actionPerformed(e);
762 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
763 neighbourTreeMenuItem
764 .addActionListener(new java.awt.event.ActionListener()
766 public void actionPerformed(ActionEvent e)
768 neighbourTreeMenuItem_actionPerformed(e);
771 this.getContentPane().setLayout(borderLayout1);
772 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
773 statusBar.setBackground(Color.white);
774 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
775 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
776 statusBar.setText("Status bar");
777 outputTextboxMenu.setText("Output to Textbox");
778 clustalColour.setText("Clustalx");
780 clustalColour.addActionListener(new java.awt.event.ActionListener()
782 public void actionPerformed(ActionEvent e)
784 clustalColour_actionPerformed(e);
787 zappoColour.setText("Zappo");
788 zappoColour.addActionListener(new java.awt.event.ActionListener()
790 public void actionPerformed(ActionEvent e)
792 zappoColour_actionPerformed(e);
795 taylorColour.setText("Taylor");
796 taylorColour.addActionListener(new java.awt.event.ActionListener()
798 public void actionPerformed(ActionEvent e)
800 taylorColour_actionPerformed(e);
803 hydrophobicityColour.setText("Hydrophobicity");
805 .addActionListener(new java.awt.event.ActionListener()
807 public void actionPerformed(ActionEvent e)
809 hydrophobicityColour_actionPerformed(e);
812 helixColour.setText("Helix Propensity");
813 helixColour.addActionListener(new java.awt.event.ActionListener()
815 public void actionPerformed(ActionEvent e)
817 helixColour_actionPerformed(e);
820 strandColour.setText("Strand Propensity");
821 strandColour.addActionListener(new java.awt.event.ActionListener()
823 public void actionPerformed(ActionEvent e)
825 strandColour_actionPerformed(e);
828 turnColour.setText("Turn Propensity");
829 turnColour.addActionListener(new java.awt.event.ActionListener()
831 public void actionPerformed(ActionEvent e)
833 turnColour_actionPerformed(e);
836 buriedColour.setText("Buried Index");
837 buriedColour.addActionListener(new java.awt.event.ActionListener()
839 public void actionPerformed(ActionEvent e)
841 buriedColour_actionPerformed(e);
844 userDefinedColour.setText("User Defined...");
845 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
847 public void actionPerformed(ActionEvent e)
849 userDefinedColour_actionPerformed(e);
852 PIDColour.setText("Percentage Identity");
853 PIDColour.addActionListener(new java.awt.event.ActionListener()
855 public void actionPerformed(ActionEvent e)
857 PIDColour_actionPerformed(e);
860 BLOSUM62Colour.setText("BLOSUM62 Score");
861 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
863 public void actionPerformed(ActionEvent e)
865 BLOSUM62Colour_actionPerformed(e);
868 nucleotideColour.setText("Nucleotide");
869 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
871 public void actionPerformed(ActionEvent e)
873 nucleotideColour_actionPerformed(e);
877 purinePyrimidineColour.setText("Purine/Pyrimidine");
878 purinePyrimidineColour
879 .addActionListener(new java.awt.event.ActionListener()
881 public void actionPerformed(ActionEvent e)
883 purinePyrimidineColour_actionPerformed(e);
887 * covariationColour.setText("Covariation");
888 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
889 * public void actionPerformed(ActionEvent e) {
890 * covariationColour_actionPerformed(e); } });
893 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
894 avDistanceTreeBlosumMenuItem
895 .addActionListener(new java.awt.event.ActionListener()
897 public void actionPerformed(ActionEvent e)
899 avTreeBlosumMenuItem_actionPerformed(e);
902 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
904 .addActionListener(new java.awt.event.ActionListener()
906 public void actionPerformed(ActionEvent e)
908 njTreeBlosumMenuItem_actionPerformed(e);
911 annotationPanelMenuItem.setActionCommand("");
912 annotationPanelMenuItem.setText("Show Annotations");
913 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
914 "SHOW_ANNOTATIONS", true));
915 annotationPanelMenuItem
916 .addActionListener(new java.awt.event.ActionListener()
918 public void actionPerformed(ActionEvent e)
920 annotationPanelMenuItem_actionPerformed(e);
923 colourTextMenuItem.setText("Colour Text");
925 .addActionListener(new java.awt.event.ActionListener()
927 public void actionPerformed(ActionEvent e)
929 colourTextMenuItem_actionPerformed(e);
932 htmlMenuItem.setText("HTML");
933 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
935 public void actionPerformed(ActionEvent e)
937 htmlMenuItem_actionPerformed(e);
940 overviewMenuItem.setText("Overview Window");
941 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
943 public void actionPerformed(ActionEvent e)
945 overviewMenuItem_actionPerformed(e);
948 undoMenuItem.setEnabled(false);
949 undoMenuItem.setText("Undo");
950 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
951 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
952 .getMenuShortcutKeyMask(), false));
953 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
955 public void actionPerformed(ActionEvent e)
957 undoMenuItem_actionPerformed(e);
960 redoMenuItem.setEnabled(false);
961 redoMenuItem.setText("Redo");
962 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
963 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
964 .getMenuShortcutKeyMask(), false));
965 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
967 public void actionPerformed(ActionEvent e)
969 redoMenuItem_actionPerformed(e);
972 conservationMenuItem.setText("By Conservation");
974 .addActionListener(new java.awt.event.ActionListener()
976 public void actionPerformed(ActionEvent e)
978 conservationMenuItem_actionPerformed(e);
981 noColourmenuItem.setText("None");
982 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
984 public void actionPerformed(ActionEvent e)
986 noColourmenuItem_actionPerformed(e);
989 wrapMenuItem.setText("Wrap");
990 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
992 public void actionPerformed(ActionEvent e)
994 wrapMenuItem_actionPerformed(e);
997 printMenuItem.setText("Print ...");
998 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
999 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1000 .getMenuShortcutKeyMask(), false));
1001 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1003 public void actionPerformed(ActionEvent e)
1005 printMenuItem_actionPerformed(e);
1008 renderGapsMenuItem.setText("Show Gaps");
1009 renderGapsMenuItem.setState(true);
1011 .addActionListener(new java.awt.event.ActionListener()
1013 public void actionPerformed(ActionEvent e)
1015 renderGapsMenuItem_actionPerformed(e);
1018 findMenuItem.setText("Find...");
1019 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1020 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1021 .getMenuShortcutKeyMask(), false));
1022 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1024 public void actionPerformed(ActionEvent e)
1026 findMenuItem_actionPerformed(e);
1029 abovePIDThreshold.setText("Above Identity Threshold");
1030 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1032 public void actionPerformed(ActionEvent e)
1034 abovePIDThreshold_actionPerformed(e);
1037 showSeqFeatures.setText("Show Sequence Features");
1038 showSeqFeatures.addActionListener(new ActionListener()
1040 public void actionPerformed(ActionEvent actionEvent)
1042 showSeqFeatures_actionPerformed(actionEvent);
1046 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1047 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1048 * void actionPerformed(ActionEvent actionEvent) {
1049 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1051 showDbRefsMenuitem.setText("Show Database Refs");
1052 showDbRefsMenuitem.addActionListener(new ActionListener()
1055 public void actionPerformed(ActionEvent e)
1057 showDbRefs_actionPerformed(e);
1061 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1062 showNpFeatsMenuitem.addActionListener(new ActionListener()
1065 public void actionPerformed(ActionEvent e)
1067 showNpFeats_actionPerformed(e);
1071 showGroupConservation.setText("Group Conservation");
1072 showGroupConservation.addActionListener(new ActionListener()
1075 public void actionPerformed(ActionEvent e)
1077 showGroupConservation_actionPerformed(e);
1082 showGroupConsensus.setText("Group Consensus");
1083 showGroupConsensus.addActionListener(new ActionListener()
1086 public void actionPerformed(ActionEvent e)
1088 showGroupConsensus_actionPerformed(e);
1092 showConsensusHistogram.setText("Show Consensus Histogram");
1093 showConsensusHistogram.addActionListener(new ActionListener()
1096 public void actionPerformed(ActionEvent e)
1098 showConsensusHistogram_actionPerformed(e);
1102 showSequenceLogo.setText("Show Consensus Logo");
1103 showSequenceLogo.addActionListener(new ActionListener()
1106 public void actionPerformed(ActionEvent e)
1108 showSequenceLogo_actionPerformed(e);
1112 applyAutoAnnotationSettings.setText("Apply to all groups");
1113 applyAutoAnnotationSettings.setState(false);
1114 applyAutoAnnotationSettings.setVisible(true);
1115 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1118 public void actionPerformed(ActionEvent e)
1120 applyAutoAnnotationSettings_actionPerformed(e);
1125 nucleotideColour.setText("Nucleotide");
1126 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1128 public void actionPerformed(ActionEvent e)
1130 nucleotideColour_actionPerformed(e);
1133 deleteGroups.setText("Undefine groups");
1134 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1135 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1136 .getMenuShortcutKeyMask(), false));
1137 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1139 public void actionPerformed(ActionEvent e)
1141 deleteGroups_actionPerformed(e);
1144 copy.setText("Copy");
1145 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1146 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1147 .getMenuShortcutKeyMask(), false));
1149 copy.addActionListener(new java.awt.event.ActionListener()
1151 public void actionPerformed(ActionEvent e)
1153 copy_actionPerformed(e);
1157 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1158 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1159 .getMenuShortcutKeyMask(), false));
1160 cut.addActionListener(new java.awt.event.ActionListener()
1162 public void actionPerformed(ActionEvent e)
1164 cut_actionPerformed(e);
1167 delete.setText("Delete");
1168 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1169 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1170 delete.addActionListener(new java.awt.event.ActionListener()
1172 public void actionPerformed(ActionEvent e)
1174 delete_actionPerformed(e);
1177 pasteMenu.setText("Paste");
1178 pasteNew.setText("To New Alignment");
1179 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1180 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1181 .getMenuShortcutKeyMask()
1182 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1183 pasteNew.addActionListener(new java.awt.event.ActionListener()
1185 public void actionPerformed(ActionEvent e)
1187 pasteNew_actionPerformed(e);
1190 pasteThis.setText("Add To This Alignment");
1191 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1192 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1193 .getMenuShortcutKeyMask(), false));
1194 pasteThis.addActionListener(new java.awt.event.ActionListener()
1196 public void actionPerformed(ActionEvent e)
1198 pasteThis_actionPerformed(e);
1201 applyToAllGroups.setText("Apply Colour To All Groups");
1202 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1204 public void actionPerformed(ActionEvent e)
1206 applyToAllGroups_actionPerformed(e);
1209 createPNG.addActionListener(new java.awt.event.ActionListener()
1211 public void actionPerformed(ActionEvent e)
1216 createPNG.setActionCommand("Save As PNG Image");
1217 createPNG.setText("PNG");
1218 font.setText("Font...");
1219 font.addActionListener(new java.awt.event.ActionListener()
1221 public void actionPerformed(ActionEvent e)
1223 font_actionPerformed(e);
1227 seqLimits.setText("Show Sequence Limits");
1228 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1229 seqLimits.addActionListener(new java.awt.event.ActionListener()
1231 public void actionPerformed(ActionEvent e)
1233 seqLimit_actionPerformed(e);
1236 epsFile.setText("EPS");
1237 epsFile.addActionListener(new java.awt.event.ActionListener()
1239 public void actionPerformed(ActionEvent e)
1244 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1245 LoadtreeMenuItem.setText("Load Associated Tree");
1246 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1248 public void actionPerformed(ActionEvent e)
1250 LoadtreeMenuItem_actionPerformed(e);
1253 scaleAbove.setVisible(false);
1254 scaleAbove.setText("Scale Above");
1255 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1257 public void actionPerformed(ActionEvent e)
1259 scaleAbove_actionPerformed(e);
1262 scaleLeft.setVisible(false);
1263 scaleLeft.setSelected(true);
1264 scaleLeft.setText("Scale Left");
1265 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1267 public void actionPerformed(ActionEvent e)
1269 scaleLeft_actionPerformed(e);
1272 scaleRight.setVisible(false);
1273 scaleRight.setSelected(true);
1274 scaleRight.setText("Scale Right");
1275 scaleRight.addActionListener(new java.awt.event.ActionListener()
1277 public void actionPerformed(ActionEvent e)
1279 scaleRight_actionPerformed(e);
1282 centreColumnLabelsMenuItem.setVisible(true);
1283 centreColumnLabelsMenuItem.setState(false);
1284 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1285 centreColumnLabelsMenuItem
1286 .addActionListener(new java.awt.event.ActionListener()
1288 public void actionPerformed(ActionEvent e)
1290 centreColumnLabels_actionPerformed(e);
1293 followHighlightMenuItem.setVisible(true);
1294 followHighlightMenuItem.setState(true);
1295 followHighlightMenuItem.setText("Automatic Scrolling");
1296 followHighlightMenuItem.addActionListener(new ActionListener()
1299 public void actionPerformed(ActionEvent e)
1301 followHighlight_actionPerformed();
1306 modifyPID.setText("Modify Identity Threshold...");
1307 modifyPID.addActionListener(new java.awt.event.ActionListener()
1309 public void actionPerformed(ActionEvent e)
1311 modifyPID_actionPerformed(e);
1314 modifyConservation.setText("Modify Conservation Threshold...");
1316 .addActionListener(new java.awt.event.ActionListener()
1318 public void actionPerformed(ActionEvent e)
1320 modifyConservation_actionPerformed(e);
1323 sortByTreeMenu.setText("By Tree Order");
1324 sort.setText("Sort");
1325 sort.addMenuListener(new MenuListener()
1327 public void menuSelected(MenuEvent e)
1332 public void menuDeselected(MenuEvent e)
1336 public void menuCanceled(MenuEvent e)
1340 sortByAnnotScore.setText("by Score");
1341 sort.add(sortByAnnotScore);
1342 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1345 public void menuCanceled(MenuEvent e)
1349 public void menuDeselected(MenuEvent e)
1353 public void menuSelected(MenuEvent e)
1355 buildSortByAnnotationScoresMenu();
1358 sortByAnnotScore.setVisible(false);
1360 calculateTree.setText("Calculate Tree");
1362 jMenu2.setText("Export Image");
1363 padGapsMenuitem.setText("Pad Gaps");
1364 padGapsMenuitem.setState(jalview.bin.Cache
1365 .getDefault("PAD_GAPS", false));
1366 padGapsMenuitem.addActionListener(new ActionListener()
1368 public void actionPerformed(ActionEvent e)
1370 padGapsMenuitem_actionPerformed(e);
1373 vamsasStore.setVisible(false);
1374 vamsasStore.setText("VAMSAS store");
1375 vamsasStore.addActionListener(new ActionListener()
1377 public void actionPerformed(ActionEvent e)
1379 vamsasStore_actionPerformed(e);
1382 showTranslation.setText("Translate cDNA");
1383 showTranslation.addActionListener(new ActionListener()
1385 public void actionPerformed(ActionEvent e)
1387 showTranslation_actionPerformed(e);
1390 extractScores.setText("Extract Scores...");
1391 extractScores.addActionListener(new ActionListener()
1393 public void actionPerformed(ActionEvent e)
1395 extractScores_actionPerformed(e);
1398 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1400 showProducts.setText("Get Cross References");
1402 * showProducts.addActionListener(new ActionListener() {
1404 * public void actionPerformed(ActionEvent e) {
1405 * showProducts_actionPerformed(e); } });
1407 featureSettings.setText("Feature Settings...");
1408 featureSettings.addActionListener(new ActionListener()
1410 public void actionPerformed(ActionEvent e)
1412 featureSettings_actionPerformed(e);
1415 fetchSequence.setText("Fetch Sequence(s)...");
1416 fetchSequence.addActionListener(new ActionListener()
1418 public void actionPerformed(ActionEvent e)
1420 fetchSequence_actionPerformed(e);
1424 annotationColour.setText("By Annotation...");
1425 annotationColour.addActionListener(new ActionListener()
1427 public void actionPerformed(ActionEvent e)
1429 annotationColour_actionPerformed(e);
1433 rnahelicesColour.setText("By RNA helices");
1434 rnahelicesColour.addActionListener(new ActionListener()
1436 public void actionPerformed(ActionEvent e)
1438 rnahelicesColour_actionPerformed(e);
1442 associatedData.setText("Load Features / Annotations");
1443 associatedData.addActionListener(new ActionListener()
1445 public void actionPerformed(ActionEvent e)
1447 associatedData_actionPerformed(e);
1450 autoCalculate.setText("Autocalculate Consensus");
1451 autoCalculate.setState(jalview.bin.Cache.getDefault(
1452 "AUTO_CALC_CONSENSUS", true));
1453 autoCalculate.addActionListener(new ActionListener()
1455 public void actionPerformed(ActionEvent e)
1457 autoCalculate_actionPerformed(e);
1460 addSequenceMenu.setText("Add Sequences");
1461 addFromFile.setText("From File");
1462 addFromFile.addActionListener(new ActionListener()
1464 public void actionPerformed(ActionEvent e)
1466 addFromFile_actionPerformed(e);
1469 addFromText.setText("From Textbox");
1470 addFromText.addActionListener(new ActionListener()
1472 public void actionPerformed(ActionEvent e)
1474 addFromText_actionPerformed(e);
1477 addFromURL.setText("From URL");
1478 addFromURL.addActionListener(new ActionListener()
1480 public void actionPerformed(ActionEvent e)
1482 addFromURL_actionPerformed(e);
1485 exportFeatures.setText("Export Features...");
1486 exportFeatures.addActionListener(new ActionListener()
1488 public void actionPerformed(ActionEvent e)
1490 exportFeatures_actionPerformed(e);
1493 exportAnnotations.setText("Export Annotations...");
1494 exportAnnotations.addActionListener(new ActionListener()
1496 public void actionPerformed(ActionEvent e)
1498 exportAnnotations_actionPerformed(e);
1501 statusPanel.setLayout(gridLayout1);
1502 jMenu3.setText("Show");
1503 showAllSeqs.setText("All Sequences");
1504 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1505 showAllSeqs.addActionListener(new ActionListener()
1507 public void actionPerformed(ActionEvent e)
1509 showAllSeqs_actionPerformed(e);
1512 showAllColumns.setText("All Columns");
1513 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1514 showAllColumns.addActionListener(new ActionListener()
1516 public void actionPerformed(ActionEvent e)
1518 showAllColumns_actionPerformed(e);
1521 hideMenu.setText("Hide");
1522 hideSelSequences.setText("Selected Sequences");
1523 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1524 hideSelSequences.addActionListener(new ActionListener()
1526 public void actionPerformed(ActionEvent e)
1528 hideSelSequences_actionPerformed(e);
1531 hideSelColumns.setText("Selected Columns");
1532 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1533 hideSelColumns.addActionListener(new ActionListener()
1535 public void actionPerformed(ActionEvent e)
1537 hideSelColumns_actionPerformed(e);
1540 hideAllSelection.setText("Selected Region");
1541 hideAllSelection.addActionListener(new ActionListener()
1543 public void actionPerformed(ActionEvent e)
1545 hideAllSelection_actionPerformed(e);
1548 // TODO: should be hidden if no selection exists.
1549 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1550 hideAllButSelection.addActionListener(new ActionListener()
1552 public void actionPerformed(ActionEvent e)
1554 hideAllButSelection_actionPerformed(e);
1557 showAllhidden.setText("All Sequences and Columns");
1559 .setToolTipText("H toggles visibility of hidden or selected regions.");
1560 showAllhidden.addActionListener(new ActionListener()
1562 public void actionPerformed(ActionEvent e)
1564 showAllhidden_actionPerformed(e);
1568 hiddenMarkers.setText("Show Hidden Markers");
1569 hiddenMarkers.addActionListener(new ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 hiddenMarkers_actionPerformed(e);
1576 invertColSel.setText("Invert Column Selection");
1577 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1578 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1579 .getMenuShortcutKeyMask()
1580 | java.awt.event.KeyEvent.ALT_MASK, false));
1581 invertColSel.addActionListener(new ActionListener()
1583 public void actionPerformed(ActionEvent e)
1585 invertColSel_actionPerformed(e);
1588 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1590 public void stateChanged(ChangeEvent evt)
1592 JTabbedPane pane = (JTabbedPane) evt.getSource();
1593 int sel = pane.getSelectedIndex();
1594 tabSelectionChanged(sel);
1597 tabbedPane.addMouseListener(new MouseAdapter()
1599 public void mousePressed(MouseEvent e)
1601 tabbedPane_mousePressed(e);
1604 tabbedPane.addFocusListener(new FocusAdapter()
1606 public void focusGained(FocusEvent e)
1608 tabbedPane_focusGained(e);
1611 save.setText("Save");
1612 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1613 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1614 .getMenuShortcutKeyMask(), false));
1615 save.addActionListener(new ActionListener()
1617 public void actionPerformed(ActionEvent e)
1619 save_actionPerformed(e);
1622 reload.setEnabled(false);
1623 reload.setText("Reload");
1624 reload.addActionListener(new ActionListener()
1626 public void actionPerformed(ActionEvent e)
1628 reload_actionPerformed(e);
1631 newView.setText("New View");
1632 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1633 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1634 .getMenuShortcutKeyMask(), false));
1635 newView.addActionListener(new ActionListener()
1637 public void actionPerformed(ActionEvent e)
1639 newView_actionPerformed(e);
1642 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1643 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1644 textColour.setText("Colour Text ...");
1645 textColour.addActionListener(new ActionListener()
1647 public void actionPerformed(ActionEvent e)
1649 textColour_actionPerformed(e);
1652 formatMenu.setText("Format");
1653 selectMenu.setText("Select");
1654 idRightAlign.setText("Right Align Sequence Id");
1655 idRightAlign.addActionListener(new ActionListener()
1657 public void actionPerformed(ActionEvent e)
1659 idRightAlign_actionPerformed(e);
1662 gatherViews.setEnabled(false);
1663 gatherViews.setText("Gather Views");
1664 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1665 java.awt.event.KeyEvent.VK_G, 0, false));
1666 gatherViews.addActionListener(new ActionListener()
1668 public void actionPerformed(ActionEvent e)
1670 gatherViews_actionPerformed(e);
1673 expandViews.setEnabled(false);
1674 expandViews.setText("Expand Views");
1675 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1676 java.awt.event.KeyEvent.VK_X, 0, false));
1677 expandViews.addActionListener(new ActionListener()
1679 public void actionPerformed(ActionEvent e)
1681 expandViews_actionPerformed(e);
1684 pageSetup.setText("Page Setup ...");
1685 pageSetup.addActionListener(new ActionListener()
1687 public void actionPerformed(ActionEvent e)
1689 pageSetup_actionPerformed(e);
1692 alignmentProperties.setText("Alignment Properties...");
1693 alignmentProperties.addActionListener(new ActionListener()
1695 public void actionPerformed(ActionEvent actionEvent)
1697 alignmentProperties();
1700 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1701 autoAnnMenu.setText("Autocalculated Annotation");
1702 alignFrameMenuBar.add(fileMenu);
1703 alignFrameMenuBar.add(editMenu);
1704 alignFrameMenuBar.add(selectMenu);
1705 alignFrameMenuBar.add(viewMenu);
1706 alignFrameMenuBar.add(formatMenu);
1707 alignFrameMenuBar.add(colourMenu);
1708 alignFrameMenuBar.add(calculateMenu);
1709 alignFrameMenuBar.add(webService);
1710 fileMenu.add(fetchSequence);
1711 fileMenu.add(addSequenceMenu);
1712 fileMenu.add(reload);
1713 fileMenu.addSeparator();
1714 fileMenu.add(vamsasStore);
1716 fileMenu.add(saveAs);
1717 fileMenu.add(outputTextboxMenu);
1718 fileMenu.add(pageSetup);
1719 fileMenu.add(printMenuItem);
1720 fileMenu.addSeparator();
1721 fileMenu.add(jMenu2);
1722 fileMenu.add(exportFeatures);
1723 fileMenu.add(exportAnnotations);
1724 fileMenu.add(LoadtreeMenuItem);
1725 fileMenu.add(associatedData);
1726 fileMenu.addSeparator();
1727 fileMenu.add(closeMenuItem);
1728 editMenu.add(undoMenuItem);
1729 editMenu.add(redoMenuItem);
1732 editMenu.add(pasteMenu);
1733 editMenu.add(delete);
1734 editMenu.addSeparator();
1735 editMenu.add(remove2LeftMenuItem);
1736 editMenu.add(remove2RightMenuItem);
1737 editMenu.add(removeGappedColumnMenuItem);
1738 editMenu.add(removeAllGapsMenuItem);
1739 editMenu.add(removeRedundancyMenuItem);
1740 editMenu.addSeparator();
1741 // dont add these yet in the CVS build - they cannot be undone!
1742 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1743 // editMenu.add(justifyLeftMenuItem);
1744 // editMenu.add(justifyRightMenuItem);
1745 // editMenu.addSeparator();
1746 editMenu.add(padGapsMenuitem);
1747 viewMenu.add(newView);
1748 viewMenu.add(expandViews);
1749 viewMenu.add(gatherViews);
1750 viewMenu.addSeparator();
1751 viewMenu.add(jMenu3);
1752 viewMenu.add(hideMenu);
1753 viewMenu.addSeparator();
1754 viewMenu.add(followHighlightMenuItem);
1755 viewMenu.add(annotationPanelMenuItem);
1756 autoAnnMenu.add(applyAutoAnnotationSettings);
1757 autoAnnMenu.add(showConsensusHistogram);
1758 autoAnnMenu.add(showSequenceLogo);
1759 autoAnnMenu.addSeparator();
1760 autoAnnMenu.add(showGroupConservation);
1761 autoAnnMenu.add(showGroupConsensus);
1762 viewMenu.add(autoAnnMenu);
1763 viewMenu.addSeparator();
1764 viewMenu.add(showSeqFeatures);
1765 // viewMenu.add(showSeqFeaturesHeight);
1767 viewMenu.add(featureSettings);
1768 tooltipSettingsMenu.add(showDbRefsMenuitem);
1769 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1770 viewMenu.add(tooltipSettingsMenu);
1771 viewMenu.addSeparator();
1772 viewMenu.add(alignmentProperties);
1773 viewMenu.addSeparator();
1774 viewMenu.add(overviewMenuItem);
1775 colourMenu.add(applyToAllGroups);
1776 colourMenu.add(textColour);
1777 colourMenu.addSeparator();
1778 colourMenu.add(noColourmenuItem);
1779 colourMenu.add(clustalColour);
1780 colourMenu.add(BLOSUM62Colour);
1781 colourMenu.add(PIDColour);
1782 colourMenu.add(zappoColour);
1783 colourMenu.add(taylorColour);
1784 colourMenu.add(hydrophobicityColour);
1785 colourMenu.add(helixColour);
1786 colourMenu.add(strandColour);
1787 colourMenu.add(turnColour);
1788 colourMenu.add(buriedColour);
1789 colourMenu.add(nucleotideColour);
1790 colourMenu.add(purinePyrimidineColour);
1791 // colourMenu.add(covariationColour);
1792 colourMenu.add(userDefinedColour);
1793 colourMenu.addSeparator();
1794 colourMenu.add(conservationMenuItem);
1795 colourMenu.add(modifyConservation);
1796 colourMenu.add(abovePIDThreshold);
1797 colourMenu.add(modifyPID);
1798 colourMenu.add(annotationColour);
1799 colourMenu.add(rnahelicesColour);
1800 calculateMenu.add(sort);
1801 calculateMenu.add(calculateTree);
1802 calculateMenu.addSeparator();
1803 calculateMenu.add(pairwiseAlignmentMenuItem);
1804 calculateMenu.add(PCAMenuItem);
1805 calculateMenu.addSeparator();
1806 calculateMenu.add(showTranslation);
1807 calculateMenu.add(showProducts);
1808 calculateMenu.add(autoCalculate);
1809 calculateMenu.addSeparator();
1810 calculateMenu.add(extractScores);
1811 webServiceNoServices = new JMenuItem("<No Services>");
1812 webService.add(webServiceNoServices);
1813 pasteMenu.add(pasteNew);
1814 pasteMenu.add(pasteThis);
1815 sort.add(sortIDMenuItem);
1816 sort.add(sortLengthMenuItem);
1817 sort.add(sortGroupMenuItem);
1818 sort.add(sortPairwiseMenuItem);
1819 sort.add(sortByTreeMenu);
1820 calculateTree.add(averageDistanceTreeMenuItem);
1821 calculateTree.add(neighbourTreeMenuItem);
1822 calculateTree.add(avDistanceTreeBlosumMenuItem);
1823 calculateTree.add(njTreeBlosumMenuItem);
1824 jMenu2.add(htmlMenuItem);
1825 jMenu2.add(epsFile);
1826 jMenu2.add(createPNG);
1827 addSequenceMenu.add(addFromFile);
1828 addSequenceMenu.add(addFromText);
1829 addSequenceMenu.add(addFromURL);
1830 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1831 statusPanel.add(statusBar, null);
1832 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1833 jMenu3.add(showAllColumns);
1834 jMenu3.add(showAllSeqs);
1835 jMenu3.add(showAllhidden);
1836 hideMenu.add(hideSelColumns);
1837 hideMenu.add(hideSelSequences);
1838 hideMenu.add(hideAllSelection);
1839 hideMenu.add(hideAllButSelection);
1841 formatMenu.add(font);
1842 formatMenu.addSeparator();
1843 formatMenu.add(wrapMenuItem);
1844 formatMenu.add(scaleAbove);
1845 formatMenu.add(scaleLeft);
1846 formatMenu.add(scaleRight);
1847 formatMenu.add(seqLimits);
1848 formatMenu.add(idRightAlign);
1849 formatMenu.add(hiddenMarkers);
1850 formatMenu.add(viewBoxesMenuItem);
1851 formatMenu.add(viewTextMenuItem);
1852 formatMenu.add(colourTextMenuItem);
1853 formatMenu.add(renderGapsMenuItem);
1854 formatMenu.add(centreColumnLabelsMenuItem);
1855 formatMenu.add(showNonconservedMenuItem);
1856 selectMenu.add(findMenuItem);
1857 selectMenu.addSeparator();
1858 selectMenu.add(selectAllSequenceMenuItem);
1859 selectMenu.add(deselectAllSequenceMenuItem);
1860 selectMenu.add(invertSequenceMenuItem);
1861 selectMenu.add(invertColSel);
1862 selectMenu.add(deleteGroups);
1863 selectMenu.add(grpsFromSelection);
1866 protected void showAllhidden_actionPerformed(ActionEvent e)
1868 // TODO Auto-generated method stub
1872 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1874 // TODO Auto-generated method stub
1878 protected void hideAllSelection_actionPerformed(ActionEvent e)
1880 // TODO Auto-generated method stub
1884 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1886 // TODO Auto-generated method stub
1890 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1892 // TODO Auto-generated method stub
1896 protected void showSequenceLogo_actionPerformed(ActionEvent e)
1898 // TODO Auto-generated method stub
1902 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1904 // TODO Auto-generated method stub
1908 protected void showGroupConsensus_actionPerformed(ActionEvent e)
1910 // TODO Auto-generated method stub
1914 protected void showGroupConservation_actionPerformed(ActionEvent e)
1916 // TODO Auto-generated method stub
1920 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1922 // TODO Auto-generated method stub
1926 protected void showSeqFeaturesHeight_actionPerformed(
1927 ActionEvent actionEvent)
1929 // TODO Auto-generated method stub
1933 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1935 // TODO Auto-generated method stub
1939 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1941 // TODO Auto-generated method stub
1945 protected void followHighlight_actionPerformed()
1947 // TODO Auto-generated method stub
1951 protected void showNpFeats_actionPerformed(ActionEvent e)
1953 // TODO Auto-generated method stub
1957 protected void showDbRefs_actionPerformed(ActionEvent e)
1959 // TODO Auto-generated method stub
1963 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1967 protected void showProducts_actionPerformed(ActionEvent e)
1971 protected void buildSortByAnnotationScoresMenu()
1975 protected void extractScores_actionPerformed(ActionEvent e)
1979 protected void outputText_actionPerformed(ActionEvent e)
1983 public void addFromFile_actionPerformed(ActionEvent e)
1988 public void addFromText_actionPerformed(ActionEvent e)
1993 public void addFromURL_actionPerformed(ActionEvent e)
1998 public void exportFeatures_actionPerformed(ActionEvent e)
2003 public void exportAnnotations_actionPerformed(ActionEvent e)
2008 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2012 protected void closeMenuItem_actionPerformed(boolean b)
2016 protected void redoMenuItem_actionPerformed(ActionEvent e)
2020 protected void undoMenuItem_actionPerformed(ActionEvent e)
2024 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2028 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2032 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2036 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2040 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2044 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2048 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2052 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2056 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2060 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2064 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2068 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2072 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2076 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2080 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2084 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2088 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2092 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2096 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2100 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2104 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2108 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2112 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2116 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2120 protected void clustalColour_actionPerformed(ActionEvent e)
2124 protected void zappoColour_actionPerformed(ActionEvent e)
2128 protected void taylorColour_actionPerformed(ActionEvent e)
2132 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2136 protected void helixColour_actionPerformed(ActionEvent e)
2140 protected void strandColour_actionPerformed(ActionEvent e)
2144 protected void turnColour_actionPerformed(ActionEvent e)
2148 protected void buriedColour_actionPerformed(ActionEvent e)
2152 protected void userDefinedColour_actionPerformed(ActionEvent e)
2156 protected void PIDColour_actionPerformed(ActionEvent e)
2160 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2164 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2169 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2172 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2176 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2180 protected void printMenuItem_actionPerformed(ActionEvent e)
2184 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2188 protected void findMenuItem_actionPerformed(ActionEvent e)
2192 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2196 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2200 protected void nucleotideColour_actionPerformed(ActionEvent e)
2204 protected void deleteGroups_actionPerformed(ActionEvent e)
2208 protected void copy_actionPerformed(ActionEvent e)
2212 protected void cut_actionPerformed(ActionEvent e)
2216 protected void delete_actionPerformed(ActionEvent e)
2220 protected void pasteNew_actionPerformed(ActionEvent e)
2224 protected void pasteThis_actionPerformed(ActionEvent e)
2228 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2232 public void createPNG(java.io.File f)
2236 protected void font_actionPerformed(ActionEvent e)
2240 protected void seqLimit_actionPerformed(ActionEvent e)
2244 public void seqDBRef_actionPerformed(ActionEvent e)
2249 public void createEPS(java.io.File f)
2253 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2257 protected void jpred_actionPerformed(ActionEvent e)
2261 protected void scaleAbove_actionPerformed(ActionEvent e)
2265 protected void scaleLeft_actionPerformed(ActionEvent e)
2269 protected void scaleRight_actionPerformed(ActionEvent e)
2273 protected void modifyPID_actionPerformed(ActionEvent e)
2277 protected void modifyConservation_actionPerformed(ActionEvent e)
2281 protected void saveAs_actionPerformed(ActionEvent e)
2285 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2289 public void vamsasStore_actionPerformed(ActionEvent e)
2294 public void vamsasLoad_actionPerformed(ActionEvent e)
2299 public void showTranslation_actionPerformed(ActionEvent e)
2304 public void featureSettings_actionPerformed(ActionEvent e)
2309 public void fetchSequence_actionPerformed(ActionEvent e)
2314 public void smoothFont_actionPerformed(ActionEvent e)
2319 public void annotationColour_actionPerformed(ActionEvent e)
2324 public void rnahelicesColour_actionPerformed(ActionEvent e)
2329 public void associatedData_actionPerformed(ActionEvent e)
2334 public void autoCalculate_actionPerformed(ActionEvent e)
2339 public void showAllSeqs_actionPerformed(ActionEvent e)
2344 public void showAllColumns_actionPerformed(ActionEvent e)
2349 public void hideSelSequences_actionPerformed(ActionEvent e)
2354 public void hideSelColumns_actionPerformed(ActionEvent e)
2359 public void hiddenMarkers_actionPerformed(ActionEvent e)
2364 public void findPdbId_actionPerformed(ActionEvent e)
2369 public void enterPdbId_actionPerformed(ActionEvent e)
2374 public void pdbFile_actionPerformed(ActionEvent e)
2379 public void invertColSel_actionPerformed(ActionEvent e)
2384 public void tabSelectionChanged(int sel)
2389 public void tabbedPane_mousePressed(MouseEvent e)
2394 public void tabbedPane_focusGained(FocusEvent e)
2399 public void save_actionPerformed(ActionEvent e)
2404 public void reload_actionPerformed(ActionEvent e)
2409 public void newView_actionPerformed(ActionEvent e)
2414 public void textColour_actionPerformed(ActionEvent e)
2419 public void idRightAlign_actionPerformed(ActionEvent e)
2424 public void expandViews_actionPerformed(ActionEvent e)
2429 public void gatherViews_actionPerformed(ActionEvent e)
2434 public void buildTreeMenu()
2439 public void pageSetup_actionPerformed(ActionEvent e)
2444 public void alignmentProperties()