2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.jbgui;
21 import java.awt.event.*;
24 import javax.swing.event.*;
26 import jalview.schemes.*;
28 public class GAlignFrame extends JInternalFrame
30 protected JMenuBar alignFrameMenuBar = new JMenuBar();
32 protected JMenu fileMenu = new JMenu();
34 protected JMenuItem closeMenuItem = new JMenuItem();
36 protected JMenu editMenu = new JMenu();
38 protected JMenu viewMenu = new JMenu();
40 protected JMenu colourMenu = new JMenu();
42 protected JMenu calculateMenu = new JMenu();
44 protected JMenu webService = new JMenu();
46 protected JMenuItem webServiceNoServices;
48 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
50 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
52 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
54 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
56 protected JMenuItem remove2RightMenuItem = new JMenuItem();
58 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
60 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
62 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
64 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
66 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
68 protected JMenuItem sortIDMenuItem = new JMenuItem();
70 protected JMenuItem sortLengthMenuItem = new JMenuItem();
72 protected JMenuItem sortGroupMenuItem = new JMenuItem();
74 protected JMenu sortByAnnotScore = new JMenu();
76 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
78 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
80 protected JMenuItem PCAMenuItem = new JMenuItem();
82 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
84 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
86 BorderLayout borderLayout1 = new BorderLayout();
88 public JLabel statusBar = new JLabel();
90 protected JMenuItem saveAs = new JMenuItem();
92 protected JMenu outputTextboxMenu = new JMenu();
94 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
96 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
98 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
100 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
102 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
104 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
106 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
108 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
110 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
112 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
114 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
116 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
118 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
120 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
122 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
124 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
126 JMenuItem htmlMenuItem = new JMenuItem();
128 JMenuItem overviewMenuItem = new JMenuItem();
130 protected JMenuItem undoMenuItem = new JMenuItem();
132 protected JMenuItem redoMenuItem = new JMenuItem();
134 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
136 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
138 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
140 JMenuItem printMenuItem = new JMenuItem();
142 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
144 JMenuItem findMenuItem = new JMenuItem();
146 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
148 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
150 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
152 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
154 JMenuItem deleteGroups = new JMenuItem();
156 JMenuItem delete = new JMenuItem();
158 JMenuItem copy = new JMenuItem();
160 JMenuItem cut = new JMenuItem();
162 JMenu pasteMenu = new JMenu();
164 JMenuItem pasteNew = new JMenuItem();
166 JMenuItem pasteThis = new JMenuItem();
168 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
170 JMenuItem createPNG = new JMenuItem();
172 protected JMenuItem font = new JMenuItem();
174 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
176 JMenuItem epsFile = new JMenuItem();
178 JMenuItem LoadtreeMenuItem = new JMenuItem();
180 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
182 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
184 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
186 protected JMenuItem modifyPID = new JMenuItem();
188 protected JMenuItem modifyConservation = new JMenuItem();
190 protected JMenu sortByTreeMenu = new JMenu();
192 protected JMenu sort = new JMenu();
194 protected JMenu calculateTree = new JMenu();
196 JMenu jMenu2 = new JMenu();
198 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
200 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
202 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
204 protected ButtonGroup colours = new ButtonGroup();
206 JMenuItem vamsasStore = new JMenuItem();
208 protected JMenuItem showTranslation = new JMenuItem();
210 protected JMenuItem extractScores = new JMenuItem();
212 protected JMenu showProducts = new JMenu();
214 public JMenuItem featureSettings = new JMenuItem();
216 JMenuItem fetchSequence = new JMenuItem();
218 JMenuItem annotationColour = new JMenuItem();
220 JMenuItem associatedData = new JMenuItem();
222 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
224 JMenu addSequenceMenu = new JMenu();
226 JMenuItem addFromFile = new JMenuItem();
228 JMenuItem addFromText = new JMenuItem();
230 JMenuItem addFromURL = new JMenuItem();
232 JMenuItem exportAnnotations = new JMenuItem();
234 JMenuItem exportFeatures = new JMenuItem();
236 protected JPanel statusPanel = new JPanel();
238 GridLayout gridLayout1 = new GridLayout();
240 JMenu jMenu3 = new JMenu();
242 JMenuItem showAllSeqs = new JMenuItem();
244 JMenuItem showAllColumns = new JMenuItem();
246 JMenu hideMenu = new JMenu();
248 JMenuItem hideSelSequences = new JMenuItem();
250 JMenuItem hideSelColumns = new JMenuItem();
252 JMenuItem hideAllButSelection = new JMenuItem();
254 JMenuItem hideAllSelection = new JMenuItem();
256 JMenuItem showAllhidden = new JMenuItem();
258 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
260 JMenuItem invertColSel = new JMenuItem();
262 protected JTabbedPane tabbedPane = new JTabbedPane();
264 JMenuItem save = new JMenuItem();
266 protected JMenuItem reload = new JMenuItem();
268 JMenuItem newView = new JMenuItem();
270 JMenuItem textColour = new JMenuItem();
272 JMenu formatMenu = new JMenu();
274 JMenu selectMenu = new JMenu();
276 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
278 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
280 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
282 protected JMenuItem gatherViews = new JMenuItem();
284 protected JMenuItem expandViews = new JMenuItem();
286 JMenuItem pageSetup = new JMenuItem();
288 JMenuItem alignmentProperties = new JMenuItem();
290 JMenu tooltipSettingsMenu = new JMenu();
292 private JMenuItem justifyLeftMenuItem = new JMenuItem();
294 private JMenuItem justifyRightMenuItem = new JMenuItem();
296 JMenu autoAnnMenu = new JMenu();
298 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
300 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
302 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
304 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
306 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
308 private JMenuItem grpsFromSelection = new JMenuItem();
315 setJMenuBar(alignFrameMenuBar);
317 // dynamically fill save as menu with available formats
318 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
320 JMenuItem item = new JMenuItem(
321 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
323 item.addActionListener(new java.awt.event.ActionListener()
325 public void actionPerformed(ActionEvent e)
327 outputText_actionPerformed(e);
331 outputTextboxMenu.add(item);
333 } catch (Exception e)
337 if (!new jalview.util.Platform().isAMac())
339 closeMenuItem.setMnemonic('C');
340 outputTextboxMenu.setMnemonic('T');
341 undoMenuItem.setMnemonic('Z');
342 redoMenuItem.setMnemonic('0');
343 copy.setMnemonic('C');
344 cut.setMnemonic('U');
345 pasteMenu.setMnemonic('P');
346 reload.setMnemonic('R');
349 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
351 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
352 .getUserColourSchemes().keys();
354 while (userColours.hasMoreElements())
356 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
357 userColours.nextElement().toString());
358 radioItem.setName("USER_DEFINED");
359 radioItem.addMouseListener(new MouseAdapter()
361 public void mousePressed(MouseEvent evt)
363 if (evt.isControlDown()
364 || SwingUtilities.isRightMouseButton(evt))
366 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
368 int option = JOptionPane.showInternalConfirmDialog(
369 jalview.gui.Desktop.desktop,
370 "Remove from default list?",
371 "Remove user defined colour",
372 JOptionPane.YES_NO_OPTION);
373 if (option == JOptionPane.YES_OPTION)
375 jalview.gui.UserDefinedColours
376 .removeColourFromDefaults(radioItem.getText());
377 colourMenu.remove(radioItem);
381 radioItem.addActionListener(new ActionListener()
383 public void actionPerformed(ActionEvent evt)
385 userDefinedColour_actionPerformed(evt);
392 radioItem.addActionListener(new ActionListener()
394 public void actionPerformed(ActionEvent evt)
396 userDefinedColour_actionPerformed(evt);
399 colourMenu.insert(radioItem, 15);
400 colours.add(radioItem);
403 colours.add(noColourmenuItem);
404 colours.add(clustalColour);
405 colours.add(zappoColour);
406 colours.add(taylorColour);
407 colours.add(hydrophobicityColour);
408 colours.add(helixColour);
409 colours.add(strandColour);
410 colours.add(turnColour);
411 colours.add(buriedColour);
412 colours.add(userDefinedColour);
413 colours.add(PIDColour);
414 colours.add(BLOSUM62Colour);
415 colours.add(nucleotideColour);
417 setColourSelected(jalview.bin.Cache
418 .getDefault("DEFAULT_COLOUR", "None"));
422 public void setColourSelected(String defaultColour)
425 if (defaultColour != null)
427 int index = ColourSchemeProperty
428 .getColourIndexFromName(defaultColour);
432 case ColourSchemeProperty.CLUSTAL:
433 clustalColour.setSelected(true);
437 case ColourSchemeProperty.BLOSUM:
438 BLOSUM62Colour.setSelected(true);
442 case ColourSchemeProperty.PID:
443 PIDColour.setSelected(true);
447 case ColourSchemeProperty.ZAPPO:
448 zappoColour.setSelected(true);
452 case ColourSchemeProperty.TAYLOR:
453 taylorColour.setSelected(true);
456 case ColourSchemeProperty.HYDROPHOBIC:
457 hydrophobicityColour.setSelected(true);
461 case ColourSchemeProperty.HELIX:
462 helixColour.setSelected(true);
466 case ColourSchemeProperty.STRAND:
467 strandColour.setSelected(true);
471 case ColourSchemeProperty.TURN:
472 turnColour.setSelected(true);
476 case ColourSchemeProperty.BURIED:
477 buriedColour.setSelected(true);
481 case ColourSchemeProperty.NUCLEOTIDE:
482 nucleotideColour.setSelected(true);
486 case ColourSchemeProperty.USER_DEFINED:
487 userDefinedColour.setSelected(true);
490 case ColourSchemeProperty.NONE:
492 noColourmenuItem.setSelected(true);
500 private void jbInit() throws Exception
502 fileMenu.setText("File");
503 saveAs.setText("Save As...");
504 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
505 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
506 .getMenuShortcutKeyMask()
507 | java.awt.event.KeyEvent.SHIFT_MASK, false));
508 saveAs.addActionListener(new ActionListener()
510 public void actionPerformed(ActionEvent e)
512 saveAs_actionPerformed(e);
515 closeMenuItem.setText("Close");
516 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
517 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
518 .getMenuShortcutKeyMask(), false));
519 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
521 public void actionPerformed(ActionEvent e)
523 closeMenuItem_actionPerformed(false);
526 editMenu.setText("Edit");
527 viewMenu.setText("View");
528 colourMenu.setText("Colour");
529 calculateMenu.setText("Calculate");
530 webService.setText("Web Service");
531 selectAllSequenceMenuItem.setText("Select All");
532 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
533 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
534 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
535 selectAllSequenceMenuItem
536 .addActionListener(new java.awt.event.ActionListener()
538 public void actionPerformed(ActionEvent e)
540 selectAllSequenceMenuItem_actionPerformed(e);
543 deselectAllSequenceMenuItem.setText("Deselect All");
544 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
545 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
546 deselectAllSequenceMenuItem
547 .addActionListener(new java.awt.event.ActionListener()
549 public void actionPerformed(ActionEvent e)
551 deselectAllSequenceMenuItem_actionPerformed(e);
554 invertSequenceMenuItem.setText("Invert Sequence Selection");
555 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
556 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
557 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
558 invertSequenceMenuItem
559 .addActionListener(new java.awt.event.ActionListener()
561 public void actionPerformed(ActionEvent e)
563 invertSequenceMenuItem_actionPerformed(e);
566 grpsFromSelection.setText("Make Groups for selection");
567 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
569 public void actionPerformed(ActionEvent e)
571 makeGrpsFromSelection_actionPerformed(e);
575 remove2LeftMenuItem.setText("Remove Left");
576 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
577 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
578 .getMenuShortcutKeyMask(), false));
580 .addActionListener(new java.awt.event.ActionListener()
582 public void actionPerformed(ActionEvent e)
584 remove2LeftMenuItem_actionPerformed(e);
587 remove2RightMenuItem.setText("Remove Right");
588 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
589 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
590 .getMenuShortcutKeyMask(), false));
592 .addActionListener(new java.awt.event.ActionListener()
594 public void actionPerformed(ActionEvent e)
596 remove2RightMenuItem_actionPerformed(e);
599 removeGappedColumnMenuItem.setText("Remove Empty Columns");
600 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
601 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
602 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
603 removeGappedColumnMenuItem
604 .addActionListener(new java.awt.event.ActionListener()
606 public void actionPerformed(ActionEvent e)
608 removeGappedColumnMenuItem_actionPerformed(e);
611 removeAllGapsMenuItem.setText("Remove All Gaps");
612 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
613 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
614 .getDefaultToolkit().getMenuShortcutKeyMask()
615 | java.awt.event.KeyEvent.SHIFT_MASK, false));
616 removeAllGapsMenuItem
617 .addActionListener(new java.awt.event.ActionListener()
619 public void actionPerformed(ActionEvent e)
621 removeAllGapsMenuItem_actionPerformed(e);
624 justifyLeftMenuItem.setText("Left Justify Alignment");
626 .addActionListener(new java.awt.event.ActionListener()
628 public void actionPerformed(ActionEvent e)
630 justifyLeftMenuItem_actionPerformed(e);
633 justifyRightMenuItem.setText("Right Justify Alignment");
635 .addActionListener(new java.awt.event.ActionListener()
637 public void actionPerformed(ActionEvent e)
639 justifyRightMenuItem_actionPerformed(e);
642 viewBoxesMenuItem.setText("Boxes");
643 viewBoxesMenuItem.setState(true);
644 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
646 public void actionPerformed(ActionEvent e)
648 viewBoxesMenuItem_actionPerformed(e);
651 viewTextMenuItem.setText("Text");
652 viewTextMenuItem.setState(true);
653 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
655 public void actionPerformed(ActionEvent e)
657 viewTextMenuItem_actionPerformed(e);
660 showNonconservedMenuItem.setText("Show nonconserved");
661 showNonconservedMenuItem.setState(false);
662 showNonconservedMenuItem
663 .addActionListener(new java.awt.event.ActionListener()
665 public void actionPerformed(ActionEvent e)
667 showUnconservedMenuItem_actionPerformed(e);
670 sortPairwiseMenuItem.setText("by Pairwise Identity");
672 .addActionListener(new java.awt.event.ActionListener()
674 public void actionPerformed(ActionEvent e)
676 sortPairwiseMenuItem_actionPerformed(e);
679 sortIDMenuItem.setText("by ID");
680 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
682 public void actionPerformed(ActionEvent e)
684 sortIDMenuItem_actionPerformed(e);
687 sortLengthMenuItem.setText("By Length");
689 .addActionListener(new java.awt.event.ActionListener()
691 public void actionPerformed(ActionEvent e)
693 sortLengthMenuItem_actionPerformed(e);
696 sortGroupMenuItem.setText("by Group");
697 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
699 public void actionPerformed(ActionEvent e)
701 sortGroupMenuItem_actionPerformed(e);
704 removeRedundancyMenuItem.setText("Remove Redundancy...");
705 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
706 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
707 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
708 removeRedundancyMenuItem
709 .addActionListener(new java.awt.event.ActionListener()
711 public void actionPerformed(ActionEvent e)
713 removeRedundancyMenuItem_actionPerformed(e);
716 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
717 pairwiseAlignmentMenuItem
718 .addActionListener(new java.awt.event.ActionListener()
720 public void actionPerformed(ActionEvent e)
722 pairwiseAlignmentMenuItem_actionPerformed(e);
725 PCAMenuItem.setText("Principal Component Analysis");
726 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
728 public void actionPerformed(ActionEvent e)
730 PCAMenuItem_actionPerformed(e);
733 averageDistanceTreeMenuItem
734 .setText("Average Distance Using % Identity");
735 averageDistanceTreeMenuItem
736 .addActionListener(new java.awt.event.ActionListener()
738 public void actionPerformed(ActionEvent e)
740 averageDistanceTreeMenuItem_actionPerformed(e);
743 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
744 neighbourTreeMenuItem
745 .addActionListener(new java.awt.event.ActionListener()
747 public void actionPerformed(ActionEvent e)
749 neighbourTreeMenuItem_actionPerformed(e);
752 this.getContentPane().setLayout(borderLayout1);
753 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
754 statusBar.setBackground(Color.white);
755 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
756 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
757 statusBar.setText("Status bar");
758 outputTextboxMenu.setText("Output to Textbox");
759 clustalColour.setText("Clustalx");
761 clustalColour.addActionListener(new java.awt.event.ActionListener()
763 public void actionPerformed(ActionEvent e)
765 clustalColour_actionPerformed(e);
768 zappoColour.setText("Zappo");
769 zappoColour.addActionListener(new java.awt.event.ActionListener()
771 public void actionPerformed(ActionEvent e)
773 zappoColour_actionPerformed(e);
776 taylorColour.setText("Taylor");
777 taylorColour.addActionListener(new java.awt.event.ActionListener()
779 public void actionPerformed(ActionEvent e)
781 taylorColour_actionPerformed(e);
784 hydrophobicityColour.setText("Hydrophobicity");
786 .addActionListener(new java.awt.event.ActionListener()
788 public void actionPerformed(ActionEvent e)
790 hydrophobicityColour_actionPerformed(e);
793 helixColour.setText("Helix Propensity");
794 helixColour.addActionListener(new java.awt.event.ActionListener()
796 public void actionPerformed(ActionEvent e)
798 helixColour_actionPerformed(e);
801 strandColour.setText("Strand Propensity");
802 strandColour.addActionListener(new java.awt.event.ActionListener()
804 public void actionPerformed(ActionEvent e)
806 strandColour_actionPerformed(e);
809 turnColour.setText("Turn Propensity");
810 turnColour.addActionListener(new java.awt.event.ActionListener()
812 public void actionPerformed(ActionEvent e)
814 turnColour_actionPerformed(e);
817 buriedColour.setText("Buried Index");
818 buriedColour.addActionListener(new java.awt.event.ActionListener()
820 public void actionPerformed(ActionEvent e)
822 buriedColour_actionPerformed(e);
825 userDefinedColour.setText("User Defined...");
826 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
828 public void actionPerformed(ActionEvent e)
830 userDefinedColour_actionPerformed(e);
833 PIDColour.setText("Percentage Identity");
834 PIDColour.addActionListener(new java.awt.event.ActionListener()
836 public void actionPerformed(ActionEvent e)
838 PIDColour_actionPerformed(e);
841 BLOSUM62Colour.setText("BLOSUM62 Score");
842 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
844 public void actionPerformed(ActionEvent e)
846 BLOSUM62Colour_actionPerformed(e);
849 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
850 avDistanceTreeBlosumMenuItem
851 .addActionListener(new java.awt.event.ActionListener()
853 public void actionPerformed(ActionEvent e)
855 avTreeBlosumMenuItem_actionPerformed(e);
858 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
860 .addActionListener(new java.awt.event.ActionListener()
862 public void actionPerformed(ActionEvent e)
864 njTreeBlosumMenuItem_actionPerformed(e);
867 annotationPanelMenuItem.setActionCommand("");
868 annotationPanelMenuItem.setText("Show Annotations");
869 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
870 "SHOW_ANNOTATIONS", true));
871 annotationPanelMenuItem
872 .addActionListener(new java.awt.event.ActionListener()
874 public void actionPerformed(ActionEvent e)
876 annotationPanelMenuItem_actionPerformed(e);
879 colourTextMenuItem.setText("Colour Text");
881 .addActionListener(new java.awt.event.ActionListener()
883 public void actionPerformed(ActionEvent e)
885 colourTextMenuItem_actionPerformed(e);
888 htmlMenuItem.setText("HTML");
889 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
891 public void actionPerformed(ActionEvent e)
893 htmlMenuItem_actionPerformed(e);
896 overviewMenuItem.setText("Overview Window");
897 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
899 public void actionPerformed(ActionEvent e)
901 overviewMenuItem_actionPerformed(e);
904 undoMenuItem.setEnabled(false);
905 undoMenuItem.setText("Undo");
906 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
907 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
908 .getMenuShortcutKeyMask(), false));
909 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
911 public void actionPerformed(ActionEvent e)
913 undoMenuItem_actionPerformed(e);
916 redoMenuItem.setEnabled(false);
917 redoMenuItem.setText("Redo");
918 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
919 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
920 .getMenuShortcutKeyMask(), false));
921 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
923 public void actionPerformed(ActionEvent e)
925 redoMenuItem_actionPerformed(e);
928 conservationMenuItem.setText("By Conservation");
930 .addActionListener(new java.awt.event.ActionListener()
932 public void actionPerformed(ActionEvent e)
934 conservationMenuItem_actionPerformed(e);
937 noColourmenuItem.setText("None");
938 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
940 public void actionPerformed(ActionEvent e)
942 noColourmenuItem_actionPerformed(e);
945 wrapMenuItem.setText("Wrap");
946 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
948 public void actionPerformed(ActionEvent e)
950 wrapMenuItem_actionPerformed(e);
953 printMenuItem.setText("Print ...");
954 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
955 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
956 .getMenuShortcutKeyMask(), false));
957 printMenuItem.addActionListener(new java.awt.event.ActionListener()
959 public void actionPerformed(ActionEvent e)
961 printMenuItem_actionPerformed(e);
964 renderGapsMenuItem.setText("Show Gaps");
965 renderGapsMenuItem.setState(true);
967 .addActionListener(new java.awt.event.ActionListener()
969 public void actionPerformed(ActionEvent e)
971 renderGapsMenuItem_actionPerformed(e);
974 findMenuItem.setText("Find...");
975 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
976 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
977 .getMenuShortcutKeyMask(), false));
978 findMenuItem.addActionListener(new java.awt.event.ActionListener()
980 public void actionPerformed(ActionEvent e)
982 findMenuItem_actionPerformed(e);
985 abovePIDThreshold.setText("Above Identity Threshold");
986 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
988 public void actionPerformed(ActionEvent e)
990 abovePIDThreshold_actionPerformed(e);
993 showSeqFeatures.setText("Show Sequence Features");
994 showSeqFeatures.addActionListener(new ActionListener()
996 public void actionPerformed(ActionEvent actionEvent)
998 showSeqFeatures_actionPerformed(actionEvent);
1002 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1003 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1004 * void actionPerformed(ActionEvent actionEvent) {
1005 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1007 showDbRefsMenuitem.setText("Show Database Refs");
1008 showDbRefsMenuitem.addActionListener(new ActionListener()
1011 public void actionPerformed(ActionEvent e)
1013 showDbRefs_actionPerformed(e);
1017 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1018 showNpFeatsMenuitem.addActionListener(new ActionListener()
1021 public void actionPerformed(ActionEvent e)
1023 showNpFeats_actionPerformed(e);
1027 showGroupConservation.setText("Group Conservation");
1028 showGroupConservation.addActionListener(new ActionListener()
1031 public void actionPerformed(ActionEvent e)
1033 showGroupConservation_actionPerformed(e);
1038 showGroupConsensus.setText("Group Consensus");
1039 showGroupConsensus.addActionListener(new ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 showGroupConsensus_actionPerformed(e);
1048 showConsensusHistogram.setText("Show Consensus Histogram");
1049 showConsensusHistogram.addActionListener(new ActionListener()
1052 public void actionPerformed(ActionEvent e)
1054 showConsensusHistogram_actionPerformed(e);
1058 showSequenceLogo.setText("Show Consensus Logo");
1059 showSequenceLogo.addActionListener(new ActionListener()
1062 public void actionPerformed(ActionEvent e)
1064 showSequenceLogo_actionPerformed(e);
1068 applyAutoAnnotationSettings.setText("Apply to all groups");
1069 applyAutoAnnotationSettings.setState(false);
1070 applyAutoAnnotationSettings.setVisible(true);
1071 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1074 public void actionPerformed(ActionEvent e)
1076 applyAutoAnnotationSettings_actionPerformed(e);
1081 nucleotideColour.setText("Nucleotide");
1082 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1084 public void actionPerformed(ActionEvent e)
1086 nucleotideColour_actionPerformed(e);
1089 deleteGroups.setText("Undefine groups");
1090 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1091 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1092 .getMenuShortcutKeyMask(), false));
1093 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1095 public void actionPerformed(ActionEvent e)
1097 deleteGroups_actionPerformed(e);
1100 copy.setText("Copy");
1101 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1102 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1103 .getMenuShortcutKeyMask(), false));
1105 copy.addActionListener(new java.awt.event.ActionListener()
1107 public void actionPerformed(ActionEvent e)
1109 copy_actionPerformed(e);
1113 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1114 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1115 .getMenuShortcutKeyMask(), false));
1116 cut.addActionListener(new java.awt.event.ActionListener()
1118 public void actionPerformed(ActionEvent e)
1120 cut_actionPerformed(e);
1123 delete.setText("Delete");
1124 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1125 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1126 delete.addActionListener(new java.awt.event.ActionListener()
1128 public void actionPerformed(ActionEvent e)
1130 delete_actionPerformed(e);
1133 pasteMenu.setText("Paste");
1134 pasteNew.setText("To New Alignment");
1135 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1136 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1137 .getMenuShortcutKeyMask()
1138 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1139 pasteNew.addActionListener(new java.awt.event.ActionListener()
1141 public void actionPerformed(ActionEvent e)
1143 pasteNew_actionPerformed(e);
1146 pasteThis.setText("Add To This Alignment");
1147 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1148 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1149 .getMenuShortcutKeyMask(), false));
1150 pasteThis.addActionListener(new java.awt.event.ActionListener()
1152 public void actionPerformed(ActionEvent e)
1154 pasteThis_actionPerformed(e);
1157 applyToAllGroups.setText("Apply Colour To All Groups");
1158 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1160 public void actionPerformed(ActionEvent e)
1162 applyToAllGroups_actionPerformed(e);
1165 createPNG.addActionListener(new java.awt.event.ActionListener()
1167 public void actionPerformed(ActionEvent e)
1172 createPNG.setActionCommand("Save As PNG Image");
1173 createPNG.setText("PNG");
1174 font.setText("Font...");
1175 font.addActionListener(new java.awt.event.ActionListener()
1177 public void actionPerformed(ActionEvent e)
1179 font_actionPerformed(e);
1183 seqLimits.setText("Show Sequence Limits");
1184 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1185 seqLimits.addActionListener(new java.awt.event.ActionListener()
1187 public void actionPerformed(ActionEvent e)
1189 seqLimit_actionPerformed(e);
1192 epsFile.setText("EPS");
1193 epsFile.addActionListener(new java.awt.event.ActionListener()
1195 public void actionPerformed(ActionEvent e)
1200 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1201 LoadtreeMenuItem.setText("Load Associated Tree");
1202 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1204 public void actionPerformed(ActionEvent e)
1206 LoadtreeMenuItem_actionPerformed(e);
1209 scaleAbove.setVisible(false);
1210 scaleAbove.setText("Scale Above");
1211 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1213 public void actionPerformed(ActionEvent e)
1215 scaleAbove_actionPerformed(e);
1218 scaleLeft.setVisible(false);
1219 scaleLeft.setSelected(true);
1220 scaleLeft.setText("Scale Left");
1221 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1223 public void actionPerformed(ActionEvent e)
1225 scaleLeft_actionPerformed(e);
1228 scaleRight.setVisible(false);
1229 scaleRight.setSelected(true);
1230 scaleRight.setText("Scale Right");
1231 scaleRight.addActionListener(new java.awt.event.ActionListener()
1233 public void actionPerformed(ActionEvent e)
1235 scaleRight_actionPerformed(e);
1238 centreColumnLabelsMenuItem.setVisible(true);
1239 centreColumnLabelsMenuItem.setState(false);
1240 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1241 centreColumnLabelsMenuItem
1242 .addActionListener(new java.awt.event.ActionListener()
1244 public void actionPerformed(ActionEvent e)
1246 centreColumnLabels_actionPerformed(e);
1249 followHighlightMenuItem.setVisible(true);
1250 followHighlightMenuItem.setState(true);
1251 followHighlightMenuItem.setText("Automatic Scrolling");
1252 followHighlightMenuItem.addActionListener(new ActionListener()
1255 public void actionPerformed(ActionEvent e)
1257 followHighlight_actionPerformed();
1262 modifyPID.setText("Modify Identity Threshold...");
1263 modifyPID.addActionListener(new java.awt.event.ActionListener()
1265 public void actionPerformed(ActionEvent e)
1267 modifyPID_actionPerformed(e);
1270 modifyConservation.setText("Modify Conservation Threshold...");
1272 .addActionListener(new java.awt.event.ActionListener()
1274 public void actionPerformed(ActionEvent e)
1276 modifyConservation_actionPerformed(e);
1279 sortByTreeMenu.setText("By Tree Order");
1280 sort.setText("Sort");
1281 sort.addMenuListener(new MenuListener()
1283 public void menuSelected(MenuEvent e)
1288 public void menuDeselected(MenuEvent e)
1292 public void menuCanceled(MenuEvent e)
1296 sortByAnnotScore.setText("by Score");
1297 sort.add(sortByAnnotScore);
1298 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1301 public void menuCanceled(MenuEvent e)
1305 public void menuDeselected(MenuEvent e)
1309 public void menuSelected(MenuEvent e)
1311 buildSortByAnnotationScoresMenu();
1314 sortByAnnotScore.setVisible(false);
1316 calculateTree.setText("Calculate Tree");
1318 jMenu2.setText("Export Image");
1319 padGapsMenuitem.setText("Pad Gaps");
1320 padGapsMenuitem.setState(jalview.bin.Cache
1321 .getDefault("PAD_GAPS", false));
1322 padGapsMenuitem.addActionListener(new ActionListener()
1324 public void actionPerformed(ActionEvent e)
1326 padGapsMenuitem_actionPerformed(e);
1329 vamsasStore.setVisible(false);
1330 vamsasStore.setText("VAMSAS store");
1331 vamsasStore.addActionListener(new ActionListener()
1333 public void actionPerformed(ActionEvent e)
1335 vamsasStore_actionPerformed(e);
1338 showTranslation.setText("Translate cDNA");
1339 showTranslation.addActionListener(new ActionListener()
1341 public void actionPerformed(ActionEvent e)
1343 showTranslation_actionPerformed(e);
1346 extractScores.setText("Extract Scores...");
1347 extractScores.addActionListener(new ActionListener()
1349 public void actionPerformed(ActionEvent e)
1351 extractScores_actionPerformed(e);
1354 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1356 showProducts.setText("Get Cross References");
1358 * showProducts.addActionListener(new ActionListener() {
1360 * public void actionPerformed(ActionEvent e) {
1361 * showProducts_actionPerformed(e); } });
1363 featureSettings.setText("Feature Settings...");
1364 featureSettings.addActionListener(new ActionListener()
1366 public void actionPerformed(ActionEvent e)
1368 featureSettings_actionPerformed(e);
1371 fetchSequence.setText("Fetch Sequence(s)...");
1372 fetchSequence.addActionListener(new ActionListener()
1374 public void actionPerformed(ActionEvent e)
1376 fetchSequence_actionPerformed(e);
1380 annotationColour.setText("By Annotation...");
1381 annotationColour.addActionListener(new ActionListener()
1383 public void actionPerformed(ActionEvent e)
1385 annotationColour_actionPerformed(e);
1388 associatedData.setText("Load Features / Annotations");
1389 associatedData.addActionListener(new ActionListener()
1391 public void actionPerformed(ActionEvent e)
1393 associatedData_actionPerformed(e);
1396 autoCalculate.setText("Autocalculate Consensus");
1397 autoCalculate.setState(jalview.bin.Cache.getDefault(
1398 "AUTO_CALC_CONSENSUS", true));
1399 autoCalculate.addActionListener(new ActionListener()
1401 public void actionPerformed(ActionEvent e)
1403 autoCalculate_actionPerformed(e);
1406 addSequenceMenu.setText("Add Sequences");
1407 addFromFile.setText("From File");
1408 addFromFile.addActionListener(new ActionListener()
1410 public void actionPerformed(ActionEvent e)
1412 addFromFile_actionPerformed(e);
1415 addFromText.setText("From Textbox");
1416 addFromText.addActionListener(new ActionListener()
1418 public void actionPerformed(ActionEvent e)
1420 addFromText_actionPerformed(e);
1423 addFromURL.setText("From URL");
1424 addFromURL.addActionListener(new ActionListener()
1426 public void actionPerformed(ActionEvent e)
1428 addFromURL_actionPerformed(e);
1431 exportFeatures.setText("Export Features...");
1432 exportFeatures.addActionListener(new ActionListener()
1434 public void actionPerformed(ActionEvent e)
1436 exportFeatures_actionPerformed(e);
1439 exportAnnotations.setText("Export Annotations...");
1440 exportAnnotations.addActionListener(new ActionListener()
1442 public void actionPerformed(ActionEvent e)
1444 exportAnnotations_actionPerformed(e);
1447 statusPanel.setLayout(gridLayout1);
1448 jMenu3.setText("Show");
1449 showAllSeqs.setText("All Sequences");
1450 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1451 showAllSeqs.addActionListener(new ActionListener()
1453 public void actionPerformed(ActionEvent e)
1455 showAllSeqs_actionPerformed(e);
1458 showAllColumns.setText("All Columns");
1459 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1460 showAllColumns.addActionListener(new ActionListener()
1462 public void actionPerformed(ActionEvent e)
1464 showAllColumns_actionPerformed(e);
1467 hideMenu.setText("Hide");
1468 hideSelSequences.setText("Selected Sequences");
1469 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1470 hideSelSequences.addActionListener(new ActionListener()
1472 public void actionPerformed(ActionEvent e)
1474 hideSelSequences_actionPerformed(e);
1477 hideSelColumns.setText("Selected Columns");
1478 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1479 hideSelColumns.addActionListener(new ActionListener()
1481 public void actionPerformed(ActionEvent e)
1483 hideSelColumns_actionPerformed(e);
1486 hideAllSelection.setText("Selected Region");
1487 hideAllSelection.addActionListener(new ActionListener()
1489 public void actionPerformed(ActionEvent e)
1491 hideAllSelection_actionPerformed(e);
1494 // TODO: should be hidden if no selection exists.
1495 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1496 hideAllButSelection.addActionListener(new ActionListener()
1498 public void actionPerformed(ActionEvent e)
1500 hideAllButSelection_actionPerformed(e);
1503 showAllhidden.setText("All Sequences and Columns");
1505 .setToolTipText("H toggles visibility of hidden or selected regions.");
1506 showAllhidden.addActionListener(new ActionListener()
1508 public void actionPerformed(ActionEvent e)
1510 showAllhidden_actionPerformed(e);
1514 hiddenMarkers.setText("Show Hidden Markers");
1515 hiddenMarkers.addActionListener(new ActionListener()
1517 public void actionPerformed(ActionEvent e)
1519 hiddenMarkers_actionPerformed(e);
1522 invertColSel.setText("Invert Column Selection");
1523 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1524 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1525 .getMenuShortcutKeyMask()
1526 | java.awt.event.KeyEvent.ALT_MASK, false));
1527 invertColSel.addActionListener(new ActionListener()
1529 public void actionPerformed(ActionEvent e)
1531 invertColSel_actionPerformed(e);
1534 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1536 public void stateChanged(ChangeEvent evt)
1538 JTabbedPane pane = (JTabbedPane) evt.getSource();
1539 int sel = pane.getSelectedIndex();
1540 tabSelectionChanged(sel);
1543 tabbedPane.addMouseListener(new MouseAdapter()
1545 public void mousePressed(MouseEvent e)
1547 tabbedPane_mousePressed(e);
1550 tabbedPane.addFocusListener(new FocusAdapter()
1552 public void focusGained(FocusEvent e)
1554 tabbedPane_focusGained(e);
1557 save.setText("Save");
1558 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1559 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1560 .getMenuShortcutKeyMask(), false));
1561 save.addActionListener(new ActionListener()
1563 public void actionPerformed(ActionEvent e)
1565 save_actionPerformed(e);
1568 reload.setEnabled(false);
1569 reload.setText("Reload");
1570 reload.addActionListener(new ActionListener()
1572 public void actionPerformed(ActionEvent e)
1574 reload_actionPerformed(e);
1577 newView.setText("New View");
1578 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1579 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1580 .getMenuShortcutKeyMask(), false));
1581 newView.addActionListener(new ActionListener()
1583 public void actionPerformed(ActionEvent e)
1585 newView_actionPerformed(e);
1588 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1589 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1590 textColour.setText("Colour Text ...");
1591 textColour.addActionListener(new ActionListener()
1593 public void actionPerformed(ActionEvent e)
1595 textColour_actionPerformed(e);
1598 formatMenu.setText("Format");
1599 selectMenu.setText("Select");
1600 idRightAlign.setText("Right Align Sequence Id");
1601 idRightAlign.addActionListener(new ActionListener()
1603 public void actionPerformed(ActionEvent e)
1605 idRightAlign_actionPerformed(e);
1608 gatherViews.setEnabled(false);
1609 gatherViews.setText("Gather Views");
1610 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1611 java.awt.event.KeyEvent.VK_G, 0, false));
1612 gatherViews.addActionListener(new ActionListener()
1614 public void actionPerformed(ActionEvent e)
1616 gatherViews_actionPerformed(e);
1619 expandViews.setEnabled(false);
1620 expandViews.setText("Expand Views");
1621 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1622 java.awt.event.KeyEvent.VK_X, 0, false));
1623 expandViews.addActionListener(new ActionListener()
1625 public void actionPerformed(ActionEvent e)
1627 expandViews_actionPerformed(e);
1630 pageSetup.setText("Page Setup ...");
1631 pageSetup.addActionListener(new ActionListener()
1633 public void actionPerformed(ActionEvent e)
1635 pageSetup_actionPerformed(e);
1638 alignmentProperties.setText("Alignment Properties...");
1639 alignmentProperties.addActionListener(new ActionListener()
1641 public void actionPerformed(ActionEvent actionEvent)
1643 alignmentProperties();
1646 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1647 autoAnnMenu.setText("Autocalculated Annotation");
1648 alignFrameMenuBar.add(fileMenu);
1649 alignFrameMenuBar.add(editMenu);
1650 alignFrameMenuBar.add(selectMenu);
1651 alignFrameMenuBar.add(viewMenu);
1652 alignFrameMenuBar.add(formatMenu);
1653 alignFrameMenuBar.add(colourMenu);
1654 alignFrameMenuBar.add(calculateMenu);
1655 alignFrameMenuBar.add(webService);
1656 fileMenu.add(fetchSequence);
1657 fileMenu.add(addSequenceMenu);
1658 fileMenu.add(reload);
1659 fileMenu.addSeparator();
1660 fileMenu.add(vamsasStore);
1662 fileMenu.add(saveAs);
1663 fileMenu.add(outputTextboxMenu);
1664 fileMenu.add(pageSetup);
1665 fileMenu.add(printMenuItem);
1666 fileMenu.addSeparator();
1667 fileMenu.add(jMenu2);
1668 fileMenu.add(exportFeatures);
1669 fileMenu.add(exportAnnotations);
1670 fileMenu.add(LoadtreeMenuItem);
1671 fileMenu.add(associatedData);
1672 fileMenu.addSeparator();
1673 fileMenu.add(closeMenuItem);
1674 editMenu.add(undoMenuItem);
1675 editMenu.add(redoMenuItem);
1678 editMenu.add(pasteMenu);
1679 editMenu.add(delete);
1680 editMenu.addSeparator();
1681 editMenu.add(remove2LeftMenuItem);
1682 editMenu.add(remove2RightMenuItem);
1683 editMenu.add(removeGappedColumnMenuItem);
1684 editMenu.add(removeAllGapsMenuItem);
1685 editMenu.add(removeRedundancyMenuItem);
1686 editMenu.addSeparator();
1687 // dont add these yet in the CVS build - they cannot be undone!
1688 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1689 // editMenu.add(justifyLeftMenuItem);
1690 // editMenu.add(justifyRightMenuItem);
1691 // editMenu.addSeparator();
1692 editMenu.add(padGapsMenuitem);
1693 viewMenu.add(newView);
1694 viewMenu.add(expandViews);
1695 viewMenu.add(gatherViews);
1696 viewMenu.addSeparator();
1697 viewMenu.add(jMenu3);
1698 viewMenu.add(hideMenu);
1699 viewMenu.addSeparator();
1700 viewMenu.add(followHighlightMenuItem);
1701 viewMenu.add(annotationPanelMenuItem);
1702 autoAnnMenu.add(applyAutoAnnotationSettings);
1703 autoAnnMenu.add(showConsensusHistogram);
1704 autoAnnMenu.add(showSequenceLogo);
1705 autoAnnMenu.addSeparator();
1706 autoAnnMenu.add(showGroupConservation);
1707 autoAnnMenu.add(showGroupConsensus);
1708 viewMenu.add(autoAnnMenu);
1709 viewMenu.addSeparator();
1710 viewMenu.add(showSeqFeatures);
1711 // viewMenu.add(showSeqFeaturesHeight);
1713 viewMenu.add(featureSettings);
1714 tooltipSettingsMenu.add(showDbRefsMenuitem);
1715 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1716 viewMenu.add(tooltipSettingsMenu);
1717 viewMenu.addSeparator();
1718 viewMenu.add(alignmentProperties);
1719 viewMenu.addSeparator();
1720 viewMenu.add(overviewMenuItem);
1721 colourMenu.add(applyToAllGroups);
1722 colourMenu.add(textColour);
1723 colourMenu.addSeparator();
1724 colourMenu.add(noColourmenuItem);
1725 colourMenu.add(clustalColour);
1726 colourMenu.add(BLOSUM62Colour);
1727 colourMenu.add(PIDColour);
1728 colourMenu.add(zappoColour);
1729 colourMenu.add(taylorColour);
1730 colourMenu.add(hydrophobicityColour);
1731 colourMenu.add(helixColour);
1732 colourMenu.add(strandColour);
1733 colourMenu.add(turnColour);
1734 colourMenu.add(buriedColour);
1735 colourMenu.add(nucleotideColour);
1736 colourMenu.add(userDefinedColour);
1737 colourMenu.addSeparator();
1738 colourMenu.add(conservationMenuItem);
1739 colourMenu.add(modifyConservation);
1740 colourMenu.add(abovePIDThreshold);
1741 colourMenu.add(modifyPID);
1742 colourMenu.add(annotationColour);
1743 calculateMenu.add(sort);
1744 calculateMenu.add(calculateTree);
1745 calculateMenu.addSeparator();
1746 calculateMenu.add(pairwiseAlignmentMenuItem);
1747 calculateMenu.add(PCAMenuItem);
1748 calculateMenu.addSeparator();
1749 calculateMenu.add(showTranslation);
1750 calculateMenu.add(showProducts);
1751 calculateMenu.add(autoCalculate);
1752 calculateMenu.addSeparator();
1753 calculateMenu.add(extractScores);
1754 webServiceNoServices = new JMenuItem("<No Services>");
1755 webService.add(webServiceNoServices);
1756 pasteMenu.add(pasteNew);
1757 pasteMenu.add(pasteThis);
1758 sort.add(sortIDMenuItem);
1759 sort.add(sortLengthMenuItem);
1760 sort.add(sortGroupMenuItem);
1761 sort.add(sortPairwiseMenuItem);
1762 sort.add(sortByTreeMenu);
1763 calculateTree.add(averageDistanceTreeMenuItem);
1764 calculateTree.add(neighbourTreeMenuItem);
1765 calculateTree.add(avDistanceTreeBlosumMenuItem);
1766 calculateTree.add(njTreeBlosumMenuItem);
1767 jMenu2.add(htmlMenuItem);
1768 jMenu2.add(epsFile);
1769 jMenu2.add(createPNG);
1770 addSequenceMenu.add(addFromFile);
1771 addSequenceMenu.add(addFromText);
1772 addSequenceMenu.add(addFromURL);
1773 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1774 statusPanel.add(statusBar, null);
1775 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1776 jMenu3.add(showAllColumns);
1777 jMenu3.add(showAllSeqs);
1778 jMenu3.add(showAllhidden);
1779 hideMenu.add(hideSelColumns);
1780 hideMenu.add(hideSelSequences);
1781 hideMenu.add(hideAllSelection);
1782 hideMenu.add(hideAllButSelection);
1784 formatMenu.add(font);
1785 formatMenu.addSeparator();
1786 formatMenu.add(wrapMenuItem);
1787 formatMenu.add(scaleAbove);
1788 formatMenu.add(scaleLeft);
1789 formatMenu.add(scaleRight);
1790 formatMenu.add(seqLimits);
1791 formatMenu.add(idRightAlign);
1792 formatMenu.add(hiddenMarkers);
1793 formatMenu.add(viewBoxesMenuItem);
1794 formatMenu.add(viewTextMenuItem);
1795 formatMenu.add(colourTextMenuItem);
1796 formatMenu.add(renderGapsMenuItem);
1797 formatMenu.add(centreColumnLabelsMenuItem);
1798 formatMenu.add(showNonconservedMenuItem);
1799 selectMenu.add(findMenuItem);
1800 selectMenu.addSeparator();
1801 selectMenu.add(selectAllSequenceMenuItem);
1802 selectMenu.add(deselectAllSequenceMenuItem);
1803 selectMenu.add(invertSequenceMenuItem);
1804 selectMenu.add(invertColSel);
1805 selectMenu.add(deleteGroups);
1806 selectMenu.add(grpsFromSelection);
1809 protected void showAllhidden_actionPerformed(ActionEvent e)
1811 // TODO Auto-generated method stub
1815 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1817 // TODO Auto-generated method stub
1821 protected void hideAllSelection_actionPerformed(ActionEvent e)
1823 // TODO Auto-generated method stub
1827 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1829 // TODO Auto-generated method stub
1833 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1835 // TODO Auto-generated method stub
1839 protected void showSequenceLogo_actionPerformed(ActionEvent e)
1841 // TODO Auto-generated method stub
1845 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1847 // TODO Auto-generated method stub
1851 protected void showGroupConsensus_actionPerformed(ActionEvent e)
1853 // TODO Auto-generated method stub
1857 protected void showGroupConservation_actionPerformed(ActionEvent e)
1859 // TODO Auto-generated method stub
1863 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1865 // TODO Auto-generated method stub
1869 protected void showSeqFeaturesHeight_actionPerformed(
1870 ActionEvent actionEvent)
1872 // TODO Auto-generated method stub
1876 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1878 // TODO Auto-generated method stub
1882 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1884 // TODO Auto-generated method stub
1888 protected void followHighlight_actionPerformed()
1890 // TODO Auto-generated method stub
1894 protected void showNpFeats_actionPerformed(ActionEvent e)
1896 // TODO Auto-generated method stub
1900 protected void showDbRefs_actionPerformed(ActionEvent e)
1902 // TODO Auto-generated method stub
1906 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1910 protected void showProducts_actionPerformed(ActionEvent e)
1914 protected void buildSortByAnnotationScoresMenu()
1918 protected void extractScores_actionPerformed(ActionEvent e)
1922 protected void outputText_actionPerformed(ActionEvent e)
1926 public void addFromFile_actionPerformed(ActionEvent e)
1931 public void addFromText_actionPerformed(ActionEvent e)
1936 public void addFromURL_actionPerformed(ActionEvent e)
1941 public void exportFeatures_actionPerformed(ActionEvent e)
1946 public void exportAnnotations_actionPerformed(ActionEvent e)
1951 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1955 protected void closeMenuItem_actionPerformed(boolean b)
1959 protected void redoMenuItem_actionPerformed(ActionEvent e)
1963 protected void undoMenuItem_actionPerformed(ActionEvent e)
1967 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1971 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1975 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1979 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1983 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1987 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1991 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1995 protected void wrapMenuItem_actionPerformed(ActionEvent e)
1999 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2003 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2007 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2011 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2015 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2019 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2023 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2027 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2031 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2035 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2039 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2043 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2047 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2051 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2055 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2059 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2063 protected void clustalColour_actionPerformed(ActionEvent e)
2067 protected void zappoColour_actionPerformed(ActionEvent e)
2071 protected void taylorColour_actionPerformed(ActionEvent e)
2075 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2079 protected void helixColour_actionPerformed(ActionEvent e)
2083 protected void strandColour_actionPerformed(ActionEvent e)
2087 protected void turnColour_actionPerformed(ActionEvent e)
2091 protected void buriedColour_actionPerformed(ActionEvent e)
2095 protected void userDefinedColour_actionPerformed(ActionEvent e)
2099 protected void PIDColour_actionPerformed(ActionEvent e)
2103 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2107 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2111 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2115 protected void printMenuItem_actionPerformed(ActionEvent e)
2119 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2123 protected void findMenuItem_actionPerformed(ActionEvent e)
2127 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2131 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2135 protected void nucleotideColour_actionPerformed(ActionEvent e)
2139 protected void deleteGroups_actionPerformed(ActionEvent e)
2143 protected void copy_actionPerformed(ActionEvent e)
2147 protected void cut_actionPerformed(ActionEvent e)
2151 protected void delete_actionPerformed(ActionEvent e)
2155 protected void pasteNew_actionPerformed(ActionEvent e)
2159 protected void pasteThis_actionPerformed(ActionEvent e)
2163 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2167 public void createPNG(java.io.File f)
2171 protected void font_actionPerformed(ActionEvent e)
2175 protected void seqLimit_actionPerformed(ActionEvent e)
2179 public void seqDBRef_actionPerformed(ActionEvent e)
2184 public void createEPS(java.io.File f)
2188 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2192 protected void jpred_actionPerformed(ActionEvent e)
2196 protected void scaleAbove_actionPerformed(ActionEvent e)
2200 protected void scaleLeft_actionPerformed(ActionEvent e)
2204 protected void scaleRight_actionPerformed(ActionEvent e)
2208 protected void modifyPID_actionPerformed(ActionEvent e)
2212 protected void modifyConservation_actionPerformed(ActionEvent e)
2216 protected void saveAs_actionPerformed(ActionEvent e)
2220 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2224 public void vamsasStore_actionPerformed(ActionEvent e)
2229 public void vamsasLoad_actionPerformed(ActionEvent e)
2234 public void showTranslation_actionPerformed(ActionEvent e)
2239 public void featureSettings_actionPerformed(ActionEvent e)
2244 public void fetchSequence_actionPerformed(ActionEvent e)
2249 public void smoothFont_actionPerformed(ActionEvent e)
2254 public void annotationColour_actionPerformed(ActionEvent e)
2259 public void associatedData_actionPerformed(ActionEvent e)
2264 public void autoCalculate_actionPerformed(ActionEvent e)
2269 public void showAllSeqs_actionPerformed(ActionEvent e)
2274 public void showAllColumns_actionPerformed(ActionEvent e)
2279 public void hideSelSequences_actionPerformed(ActionEvent e)
2284 public void hideSelColumns_actionPerformed(ActionEvent e)
2289 public void hiddenMarkers_actionPerformed(ActionEvent e)
2294 public void findPdbId_actionPerformed(ActionEvent e)
2299 public void enterPdbId_actionPerformed(ActionEvent e)
2304 public void pdbFile_actionPerformed(ActionEvent e)
2309 public void invertColSel_actionPerformed(ActionEvent e)
2314 public void tabSelectionChanged(int sel)
2319 public void tabbedPane_mousePressed(MouseEvent e)
2324 public void tabbedPane_focusGained(FocusEvent e)
2329 public void save_actionPerformed(ActionEvent e)
2334 public void reload_actionPerformed(ActionEvent e)
2339 public void newView_actionPerformed(ActionEvent e)
2344 public void textColour_actionPerformed(ActionEvent e)
2349 public void idRightAlign_actionPerformed(ActionEvent e)
2354 public void expandViews_actionPerformed(ActionEvent e)
2359 public void gatherViews_actionPerformed(ActionEvent e)
2364 public void buildTreeMenu()
2369 public void pageSetup_actionPerformed(ActionEvent e)
2374 public void alignmentProperties()