2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.jbgui;
21 import java.awt.event.*;
24 import javax.swing.event.*;
26 import jalview.schemes.*;
28 public class GAlignFrame extends JInternalFrame
30 protected JMenuBar alignFrameMenuBar = new JMenuBar();
32 protected JMenu fileMenu = new JMenu();
34 protected JMenuItem closeMenuItem = new JMenuItem();
36 protected JMenu editMenu = new JMenu();
38 protected JMenu viewMenu = new JMenu();
40 protected JMenu colourMenu = new JMenu();
42 protected JMenu calculateMenu = new JMenu();
44 protected JMenu webService = new JMenu();
46 protected JMenuItem webServiceNoServices;
48 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
50 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
52 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
54 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
56 protected JMenuItem remove2RightMenuItem = new JMenuItem();
58 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
60 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
62 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
64 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
66 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
68 protected JMenuItem sortIDMenuItem = new JMenuItem();
70 protected JMenuItem sortLengthMenuItem = new JMenuItem();
72 protected JMenuItem sortGroupMenuItem = new JMenuItem();
74 protected JMenu sortByAnnotScore = new JMenu();
76 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
78 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
80 protected JMenuItem PCAMenuItem = new JMenuItem();
82 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
84 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
86 BorderLayout borderLayout1 = new BorderLayout();
88 public JLabel statusBar = new JLabel();
90 protected JMenuItem saveAs = new JMenuItem();
92 protected JMenu outputTextboxMenu = new JMenu();
94 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
96 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
98 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
100 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
102 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
104 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
106 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
108 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
110 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
112 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
114 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
116 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
118 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
120 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
122 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
124 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
126 JMenuItem htmlMenuItem = new JMenuItem();
128 JMenuItem overviewMenuItem = new JMenuItem();
130 protected JMenuItem undoMenuItem = new JMenuItem();
132 protected JMenuItem redoMenuItem = new JMenuItem();
134 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
136 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
138 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
140 JMenuItem printMenuItem = new JMenuItem();
142 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
144 JMenuItem findMenuItem = new JMenuItem();
146 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
148 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
150 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
152 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
154 JMenuItem deleteGroups = new JMenuItem();
156 JMenuItem delete = new JMenuItem();
158 JMenuItem copy = new JMenuItem();
160 JMenuItem cut = new JMenuItem();
162 JMenu pasteMenu = new JMenu();
164 JMenuItem pasteNew = new JMenuItem();
166 JMenuItem pasteThis = new JMenuItem();
168 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
170 JMenuItem createPNG = new JMenuItem();
172 protected JMenuItem font = new JMenuItem();
174 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
176 JMenuItem epsFile = new JMenuItem();
178 JMenuItem LoadtreeMenuItem = new JMenuItem();
180 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
182 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
184 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
186 protected JMenuItem modifyPID = new JMenuItem();
188 protected JMenuItem modifyConservation = new JMenuItem();
190 protected JMenu sortByTreeMenu = new JMenu();
192 protected JMenu sort = new JMenu();
194 protected JMenu calculateTree = new JMenu();
196 JMenu jMenu2 = new JMenu();
198 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
200 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
202 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
204 protected ButtonGroup colours = new ButtonGroup();
206 JMenuItem vamsasStore = new JMenuItem();
208 protected JMenuItem showTranslation = new JMenuItem();
210 protected JMenuItem extractScores = new JMenuItem();
212 protected JMenu showProducts = new JMenu();
214 public JMenuItem featureSettings = new JMenuItem();
216 JMenuItem fetchSequence = new JMenuItem();
218 JMenuItem annotationColour = new JMenuItem();
220 JMenuItem associatedData = new JMenuItem();
222 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
224 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
226 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
228 JMenu addSequenceMenu = new JMenu();
230 JMenuItem addFromFile = new JMenuItem();
232 JMenuItem addFromText = new JMenuItem();
234 JMenuItem addFromURL = new JMenuItem();
236 JMenuItem exportAnnotations = new JMenuItem();
238 JMenuItem exportFeatures = new JMenuItem();
240 protected JPanel statusPanel = new JPanel();
242 GridLayout gridLayout1 = new GridLayout();
244 JMenu jMenu3 = new JMenu();
246 JMenuItem showAllSeqs = new JMenuItem();
248 JMenuItem showAllColumns = new JMenuItem();
250 JMenu hideMenu = new JMenu();
252 JMenuItem hideSelSequences = new JMenuItem();
254 JMenuItem hideSelColumns = new JMenuItem();
256 JMenuItem hideAllButSelection = new JMenuItem();
258 JMenuItem hideAllSelection = new JMenuItem();
260 JMenuItem showAllhidden = new JMenuItem();
262 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
264 JMenuItem invertColSel = new JMenuItem();
266 protected JTabbedPane tabbedPane = new JTabbedPane();
268 JMenuItem save = new JMenuItem();
270 protected JMenuItem reload = new JMenuItem();
272 JMenuItem newView = new JMenuItem();
274 JMenuItem textColour = new JMenuItem();
276 JMenu formatMenu = new JMenu();
278 JMenu selectMenu = new JMenu();
280 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
282 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
284 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
286 protected JMenuItem gatherViews = new JMenuItem();
288 protected JMenuItem expandViews = new JMenuItem();
290 JMenuItem pageSetup = new JMenuItem();
292 JMenuItem alignmentProperties = new JMenuItem();
294 JMenu tooltipSettingsMenu = new JMenu();
296 private JMenuItem justifyLeftMenuItem = new JMenuItem();
298 private JMenuItem justifyRightMenuItem = new JMenuItem();
300 JMenu autoAnnMenu = new JMenu();
302 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
304 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
306 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
308 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
310 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
312 private JMenuItem grpsFromSelection = new JMenuItem();
319 setJMenuBar(alignFrameMenuBar);
321 // dynamically fill save as menu with available formats
322 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
324 JMenuItem item = new JMenuItem(
325 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
327 item.addActionListener(new java.awt.event.ActionListener()
329 public void actionPerformed(ActionEvent e)
331 outputText_actionPerformed(e);
335 outputTextboxMenu.add(item);
337 } catch (Exception e)
341 if (!new jalview.util.Platform().isAMac())
343 closeMenuItem.setMnemonic('C');
344 outputTextboxMenu.setMnemonic('T');
345 undoMenuItem.setMnemonic('Z');
346 redoMenuItem.setMnemonic('0');
347 copy.setMnemonic('C');
348 cut.setMnemonic('U');
349 pasteMenu.setMnemonic('P');
350 reload.setMnemonic('R');
353 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
355 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
356 .getUserColourSchemes().keys();
358 while (userColours.hasMoreElements())
360 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
361 userColours.nextElement().toString());
362 radioItem.setName("USER_DEFINED");
363 radioItem.addMouseListener(new MouseAdapter()
365 public void mousePressed(MouseEvent evt)
367 if (evt.isControlDown()
368 || SwingUtilities.isRightMouseButton(evt))
370 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
372 int option = JOptionPane.showInternalConfirmDialog(
373 jalview.gui.Desktop.desktop,
374 "Remove from default list?",
375 "Remove user defined colour",
376 JOptionPane.YES_NO_OPTION);
377 if (option == JOptionPane.YES_OPTION)
379 jalview.gui.UserDefinedColours
380 .removeColourFromDefaults(radioItem.getText());
381 colourMenu.remove(radioItem);
385 radioItem.addActionListener(new ActionListener()
387 public void actionPerformed(ActionEvent evt)
389 userDefinedColour_actionPerformed(evt);
396 radioItem.addActionListener(new ActionListener()
398 public void actionPerformed(ActionEvent evt)
400 userDefinedColour_actionPerformed(evt);
403 colourMenu.insert(radioItem, 15);
404 colours.add(radioItem);
407 colours.add(noColourmenuItem);
408 colours.add(clustalColour);
409 colours.add(zappoColour);
410 colours.add(taylorColour);
411 colours.add(hydrophobicityColour);
412 colours.add(helixColour);
413 colours.add(strandColour);
414 colours.add(turnColour);
415 colours.add(buriedColour);
416 colours.add(userDefinedColour);
417 colours.add(PIDColour);
418 colours.add(BLOSUM62Colour);
419 colours.add(nucleotideColour);
421 setColourSelected(jalview.bin.Cache
422 .getDefault("DEFAULT_COLOUR", "None"));
426 public void setColourSelected(String defaultColour)
429 if (defaultColour != null)
431 int index = ColourSchemeProperty
432 .getColourIndexFromName(defaultColour);
436 case ColourSchemeProperty.CLUSTAL:
437 clustalColour.setSelected(true);
441 case ColourSchemeProperty.BLOSUM:
442 BLOSUM62Colour.setSelected(true);
446 case ColourSchemeProperty.PID:
447 PIDColour.setSelected(true);
451 case ColourSchemeProperty.ZAPPO:
452 zappoColour.setSelected(true);
456 case ColourSchemeProperty.TAYLOR:
457 taylorColour.setSelected(true);
460 case ColourSchemeProperty.HYDROPHOBIC:
461 hydrophobicityColour.setSelected(true);
465 case ColourSchemeProperty.HELIX:
466 helixColour.setSelected(true);
470 case ColourSchemeProperty.STRAND:
471 strandColour.setSelected(true);
475 case ColourSchemeProperty.TURN:
476 turnColour.setSelected(true);
480 case ColourSchemeProperty.BURIED:
481 buriedColour.setSelected(true);
485 case ColourSchemeProperty.NUCLEOTIDE:
486 nucleotideColour.setSelected(true);
490 case ColourSchemeProperty.USER_DEFINED:
491 userDefinedColour.setSelected(true);
494 case ColourSchemeProperty.NONE:
496 noColourmenuItem.setSelected(true);
504 private void jbInit() throws Exception
506 fileMenu.setText("File");
507 saveAs.setText("Save As...");
508 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
509 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
510 .getMenuShortcutKeyMask()
511 | java.awt.event.KeyEvent.SHIFT_MASK, false));
512 saveAs.addActionListener(new ActionListener()
514 public void actionPerformed(ActionEvent e)
516 saveAs_actionPerformed(e);
519 closeMenuItem.setText("Close");
520 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
521 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
522 .getMenuShortcutKeyMask(), false));
523 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
525 public void actionPerformed(ActionEvent e)
527 closeMenuItem_actionPerformed(false);
530 editMenu.setText("Edit");
531 viewMenu.setText("View");
532 colourMenu.setText("Colour");
533 calculateMenu.setText("Calculate");
534 webService.setText("Web Service");
535 selectAllSequenceMenuItem.setText("Select All");
536 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
537 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
538 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
539 selectAllSequenceMenuItem
540 .addActionListener(new java.awt.event.ActionListener()
542 public void actionPerformed(ActionEvent e)
544 selectAllSequenceMenuItem_actionPerformed(e);
547 deselectAllSequenceMenuItem.setText("Deselect All");
548 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
549 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
550 deselectAllSequenceMenuItem
551 .addActionListener(new java.awt.event.ActionListener()
553 public void actionPerformed(ActionEvent e)
555 deselectAllSequenceMenuItem_actionPerformed(e);
558 invertSequenceMenuItem.setText("Invert Sequence Selection");
559 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
560 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
561 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
562 invertSequenceMenuItem
563 .addActionListener(new java.awt.event.ActionListener()
565 public void actionPerformed(ActionEvent e)
567 invertSequenceMenuItem_actionPerformed(e);
570 grpsFromSelection.setText("Make Groups for selection");
571 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
573 public void actionPerformed(ActionEvent e)
575 makeGrpsFromSelection_actionPerformed(e);
579 remove2LeftMenuItem.setText("Remove Left");
580 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
581 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
582 .getMenuShortcutKeyMask(), false));
584 .addActionListener(new java.awt.event.ActionListener()
586 public void actionPerformed(ActionEvent e)
588 remove2LeftMenuItem_actionPerformed(e);
591 remove2RightMenuItem.setText("Remove Right");
592 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
593 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
594 .getMenuShortcutKeyMask(), false));
596 .addActionListener(new java.awt.event.ActionListener()
598 public void actionPerformed(ActionEvent e)
600 remove2RightMenuItem_actionPerformed(e);
603 removeGappedColumnMenuItem.setText("Remove Empty Columns");
604 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
605 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
606 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
607 removeGappedColumnMenuItem
608 .addActionListener(new java.awt.event.ActionListener()
610 public void actionPerformed(ActionEvent e)
612 removeGappedColumnMenuItem_actionPerformed(e);
615 removeAllGapsMenuItem.setText("Remove All Gaps");
616 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
617 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
618 .getDefaultToolkit().getMenuShortcutKeyMask()
619 | java.awt.event.KeyEvent.SHIFT_MASK, false));
620 removeAllGapsMenuItem
621 .addActionListener(new java.awt.event.ActionListener()
623 public void actionPerformed(ActionEvent e)
625 removeAllGapsMenuItem_actionPerformed(e);
628 justifyLeftMenuItem.setText("Left Justify Alignment");
630 .addActionListener(new java.awt.event.ActionListener()
632 public void actionPerformed(ActionEvent e)
634 justifyLeftMenuItem_actionPerformed(e);
637 justifyRightMenuItem.setText("Right Justify Alignment");
639 .addActionListener(new java.awt.event.ActionListener()
641 public void actionPerformed(ActionEvent e)
643 justifyRightMenuItem_actionPerformed(e);
646 viewBoxesMenuItem.setText("Boxes");
647 viewBoxesMenuItem.setState(true);
648 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
650 public void actionPerformed(ActionEvent e)
652 viewBoxesMenuItem_actionPerformed(e);
655 viewTextMenuItem.setText("Text");
656 viewTextMenuItem.setState(true);
657 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
659 public void actionPerformed(ActionEvent e)
661 viewTextMenuItem_actionPerformed(e);
664 showNonconservedMenuItem.setText("Show nonconserved");
665 showNonconservedMenuItem.setState(false);
666 showNonconservedMenuItem
667 .addActionListener(new java.awt.event.ActionListener()
669 public void actionPerformed(ActionEvent e)
671 showUnconservedMenuItem_actionPerformed(e);
674 sortPairwiseMenuItem.setText("by Pairwise Identity");
676 .addActionListener(new java.awt.event.ActionListener()
678 public void actionPerformed(ActionEvent e)
680 sortPairwiseMenuItem_actionPerformed(e);
683 sortIDMenuItem.setText("by ID");
684 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
686 public void actionPerformed(ActionEvent e)
688 sortIDMenuItem_actionPerformed(e);
691 sortLengthMenuItem.setText("By Length");
693 .addActionListener(new java.awt.event.ActionListener()
695 public void actionPerformed(ActionEvent e)
697 sortLengthMenuItem_actionPerformed(e);
700 sortGroupMenuItem.setText("by Group");
701 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
703 public void actionPerformed(ActionEvent e)
705 sortGroupMenuItem_actionPerformed(e);
708 removeRedundancyMenuItem.setText("Remove Redundancy...");
709 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
710 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
711 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
712 removeRedundancyMenuItem
713 .addActionListener(new java.awt.event.ActionListener()
715 public void actionPerformed(ActionEvent e)
717 removeRedundancyMenuItem_actionPerformed(e);
720 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
721 pairwiseAlignmentMenuItem
722 .addActionListener(new java.awt.event.ActionListener()
724 public void actionPerformed(ActionEvent e)
726 pairwiseAlignmentMenuItem_actionPerformed(e);
729 PCAMenuItem.setText("Principal Component Analysis");
730 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
732 public void actionPerformed(ActionEvent e)
734 PCAMenuItem_actionPerformed(e);
737 averageDistanceTreeMenuItem
738 .setText("Average Distance Using % Identity");
739 averageDistanceTreeMenuItem
740 .addActionListener(new java.awt.event.ActionListener()
742 public void actionPerformed(ActionEvent e)
744 averageDistanceTreeMenuItem_actionPerformed(e);
747 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
748 neighbourTreeMenuItem
749 .addActionListener(new java.awt.event.ActionListener()
751 public void actionPerformed(ActionEvent e)
753 neighbourTreeMenuItem_actionPerformed(e);
756 this.getContentPane().setLayout(borderLayout1);
757 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
758 statusBar.setBackground(Color.white);
759 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
760 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
761 statusBar.setText("Status bar");
762 outputTextboxMenu.setText("Output to Textbox");
763 clustalColour.setText("Clustalx");
765 clustalColour.addActionListener(new java.awt.event.ActionListener()
767 public void actionPerformed(ActionEvent e)
769 clustalColour_actionPerformed(e);
772 zappoColour.setText("Zappo");
773 zappoColour.addActionListener(new java.awt.event.ActionListener()
775 public void actionPerformed(ActionEvent e)
777 zappoColour_actionPerformed(e);
780 taylorColour.setText("Taylor");
781 taylorColour.addActionListener(new java.awt.event.ActionListener()
783 public void actionPerformed(ActionEvent e)
785 taylorColour_actionPerformed(e);
788 hydrophobicityColour.setText("Hydrophobicity");
790 .addActionListener(new java.awt.event.ActionListener()
792 public void actionPerformed(ActionEvent e)
794 hydrophobicityColour_actionPerformed(e);
797 helixColour.setText("Helix Propensity");
798 helixColour.addActionListener(new java.awt.event.ActionListener()
800 public void actionPerformed(ActionEvent e)
802 helixColour_actionPerformed(e);
805 strandColour.setText("Strand Propensity");
806 strandColour.addActionListener(new java.awt.event.ActionListener()
808 public void actionPerformed(ActionEvent e)
810 strandColour_actionPerformed(e);
813 turnColour.setText("Turn Propensity");
814 turnColour.addActionListener(new java.awt.event.ActionListener()
816 public void actionPerformed(ActionEvent e)
818 turnColour_actionPerformed(e);
821 buriedColour.setText("Buried Index");
822 buriedColour.addActionListener(new java.awt.event.ActionListener()
824 public void actionPerformed(ActionEvent e)
826 buriedColour_actionPerformed(e);
829 userDefinedColour.setText("User Defined...");
830 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
832 public void actionPerformed(ActionEvent e)
834 userDefinedColour_actionPerformed(e);
837 PIDColour.setText("Percentage Identity");
838 PIDColour.addActionListener(new java.awt.event.ActionListener()
840 public void actionPerformed(ActionEvent e)
842 PIDColour_actionPerformed(e);
845 BLOSUM62Colour.setText("BLOSUM62 Score");
846 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
848 public void actionPerformed(ActionEvent e)
850 BLOSUM62Colour_actionPerformed(e);
853 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
854 avDistanceTreeBlosumMenuItem
855 .addActionListener(new java.awt.event.ActionListener()
857 public void actionPerformed(ActionEvent e)
859 avTreeBlosumMenuItem_actionPerformed(e);
862 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
864 .addActionListener(new java.awt.event.ActionListener()
866 public void actionPerformed(ActionEvent e)
868 njTreeBlosumMenuItem_actionPerformed(e);
871 annotationPanelMenuItem.setActionCommand("");
872 annotationPanelMenuItem.setText("Show Annotations");
873 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
874 "SHOW_ANNOTATIONS", true));
875 annotationPanelMenuItem
876 .addActionListener(new java.awt.event.ActionListener()
878 public void actionPerformed(ActionEvent e)
880 annotationPanelMenuItem_actionPerformed(e);
883 colourTextMenuItem.setText("Colour Text");
885 .addActionListener(new java.awt.event.ActionListener()
887 public void actionPerformed(ActionEvent e)
889 colourTextMenuItem_actionPerformed(e);
892 htmlMenuItem.setText("HTML");
893 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
895 public void actionPerformed(ActionEvent e)
897 htmlMenuItem_actionPerformed(e);
900 overviewMenuItem.setText("Overview Window");
901 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
903 public void actionPerformed(ActionEvent e)
905 overviewMenuItem_actionPerformed(e);
908 undoMenuItem.setEnabled(false);
909 undoMenuItem.setText("Undo");
910 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
911 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
912 .getMenuShortcutKeyMask(), false));
913 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
915 public void actionPerformed(ActionEvent e)
917 undoMenuItem_actionPerformed(e);
920 redoMenuItem.setEnabled(false);
921 redoMenuItem.setText("Redo");
922 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
923 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
924 .getMenuShortcutKeyMask(), false));
925 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
927 public void actionPerformed(ActionEvent e)
929 redoMenuItem_actionPerformed(e);
932 conservationMenuItem.setText("By Conservation");
934 .addActionListener(new java.awt.event.ActionListener()
936 public void actionPerformed(ActionEvent e)
938 conservationMenuItem_actionPerformed(e);
941 noColourmenuItem.setText("None");
942 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
944 public void actionPerformed(ActionEvent e)
946 noColourmenuItem_actionPerformed(e);
949 wrapMenuItem.setText("Wrap");
950 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
952 public void actionPerformed(ActionEvent e)
954 wrapMenuItem_actionPerformed(e);
957 printMenuItem.setText("Print ...");
958 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
959 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
960 .getMenuShortcutKeyMask(), false));
961 printMenuItem.addActionListener(new java.awt.event.ActionListener()
963 public void actionPerformed(ActionEvent e)
965 printMenuItem_actionPerformed(e);
968 renderGapsMenuItem.setText("Show Gaps");
969 renderGapsMenuItem.setState(true);
971 .addActionListener(new java.awt.event.ActionListener()
973 public void actionPerformed(ActionEvent e)
975 renderGapsMenuItem_actionPerformed(e);
978 findMenuItem.setText("Find...");
979 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
980 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
981 .getMenuShortcutKeyMask(), false));
982 findMenuItem.addActionListener(new java.awt.event.ActionListener()
984 public void actionPerformed(ActionEvent e)
986 findMenuItem_actionPerformed(e);
989 abovePIDThreshold.setText("Above Identity Threshold");
990 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
992 public void actionPerformed(ActionEvent e)
994 abovePIDThreshold_actionPerformed(e);
997 showSeqFeatures.setText("Show Sequence Features");
998 showSeqFeatures.addActionListener(new ActionListener()
1000 public void actionPerformed(ActionEvent actionEvent)
1002 showSeqFeatures_actionPerformed(actionEvent);
1006 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1007 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1008 * void actionPerformed(ActionEvent actionEvent) {
1009 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1011 showDbRefsMenuitem.setText("Show Database Refs");
1012 showDbRefsMenuitem.addActionListener(new ActionListener()
1015 public void actionPerformed(ActionEvent e)
1017 showDbRefs_actionPerformed(e);
1021 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1022 showNpFeatsMenuitem.addActionListener(new ActionListener()
1025 public void actionPerformed(ActionEvent e)
1027 showNpFeats_actionPerformed(e);
1031 showGroupConservation.setText("Group Conservation");
1032 showGroupConservation.addActionListener(new ActionListener()
1035 public void actionPerformed(ActionEvent e)
1037 showGroupConservation_actionPerformed(e);
1042 showGroupConsensus.setText("Group Consensus");
1043 showGroupConsensus.addActionListener(new ActionListener()
1046 public void actionPerformed(ActionEvent e)
1048 showGroupConsensus_actionPerformed(e);
1052 showConsensusHistogram.setText("Show Consensus Histogram");
1053 showConsensusHistogram.addActionListener(new ActionListener()
1056 public void actionPerformed(ActionEvent e)
1058 showConsensusHistogram_actionPerformed(e);
1062 showSequenceLogo.setText("Show Consensus Logo");
1063 showSequenceLogo.addActionListener(new ActionListener()
1066 public void actionPerformed(ActionEvent e)
1068 showSequenceLogo_actionPerformed(e);
1072 applyAutoAnnotationSettings.setText("Apply to all groups");
1073 applyAutoAnnotationSettings.setState(false);
1074 applyAutoAnnotationSettings.setVisible(true);
1075 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1078 public void actionPerformed(ActionEvent e)
1080 applyAutoAnnotationSettings_actionPerformed(e);
1085 nucleotideColour.setText("Nucleotide");
1086 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1088 public void actionPerformed(ActionEvent e)
1090 nucleotideColour_actionPerformed(e);
1093 deleteGroups.setText("Undefine groups");
1094 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1095 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1096 .getMenuShortcutKeyMask(), false));
1097 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1099 public void actionPerformed(ActionEvent e)
1101 deleteGroups_actionPerformed(e);
1104 copy.setText("Copy");
1105 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1106 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1107 .getMenuShortcutKeyMask(), false));
1109 copy.addActionListener(new java.awt.event.ActionListener()
1111 public void actionPerformed(ActionEvent e)
1113 copy_actionPerformed(e);
1117 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1118 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1119 .getMenuShortcutKeyMask(), false));
1120 cut.addActionListener(new java.awt.event.ActionListener()
1122 public void actionPerformed(ActionEvent e)
1124 cut_actionPerformed(e);
1127 delete.setText("Delete");
1128 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1129 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1130 delete.addActionListener(new java.awt.event.ActionListener()
1132 public void actionPerformed(ActionEvent e)
1134 delete_actionPerformed(e);
1137 pasteMenu.setText("Paste");
1138 pasteNew.setText("To New Alignment");
1139 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1140 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1141 .getMenuShortcutKeyMask()
1142 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1143 pasteNew.addActionListener(new java.awt.event.ActionListener()
1145 public void actionPerformed(ActionEvent e)
1147 pasteNew_actionPerformed(e);
1150 pasteThis.setText("Add To This Alignment");
1151 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1152 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1153 .getMenuShortcutKeyMask(), false));
1154 pasteThis.addActionListener(new java.awt.event.ActionListener()
1156 public void actionPerformed(ActionEvent e)
1158 pasteThis_actionPerformed(e);
1161 applyToAllGroups.setText("Apply Colour To All Groups");
1162 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1164 public void actionPerformed(ActionEvent e)
1166 applyToAllGroups_actionPerformed(e);
1169 createPNG.addActionListener(new java.awt.event.ActionListener()
1171 public void actionPerformed(ActionEvent e)
1176 createPNG.setActionCommand("Save As PNG Image");
1177 createPNG.setText("PNG");
1178 font.setText("Font...");
1179 font.addActionListener(new java.awt.event.ActionListener()
1181 public void actionPerformed(ActionEvent e)
1183 font_actionPerformed(e);
1187 seqLimits.setText("Show Sequence Limits");
1188 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1189 seqLimits.addActionListener(new java.awt.event.ActionListener()
1191 public void actionPerformed(ActionEvent e)
1193 seqLimit_actionPerformed(e);
1196 epsFile.setText("EPS");
1197 epsFile.addActionListener(new java.awt.event.ActionListener()
1199 public void actionPerformed(ActionEvent e)
1204 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1205 LoadtreeMenuItem.setText("Load Associated Tree");
1206 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1208 public void actionPerformed(ActionEvent e)
1210 LoadtreeMenuItem_actionPerformed(e);
1213 scaleAbove.setVisible(false);
1214 scaleAbove.setText("Scale Above");
1215 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1217 public void actionPerformed(ActionEvent e)
1219 scaleAbove_actionPerformed(e);
1222 scaleLeft.setVisible(false);
1223 scaleLeft.setSelected(true);
1224 scaleLeft.setText("Scale Left");
1225 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1227 public void actionPerformed(ActionEvent e)
1229 scaleLeft_actionPerformed(e);
1232 scaleRight.setVisible(false);
1233 scaleRight.setSelected(true);
1234 scaleRight.setText("Scale Right");
1235 scaleRight.addActionListener(new java.awt.event.ActionListener()
1237 public void actionPerformed(ActionEvent e)
1239 scaleRight_actionPerformed(e);
1242 centreColumnLabelsMenuItem.setVisible(true);
1243 centreColumnLabelsMenuItem.setState(false);
1244 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1245 centreColumnLabelsMenuItem
1246 .addActionListener(new java.awt.event.ActionListener()
1248 public void actionPerformed(ActionEvent e)
1250 centreColumnLabels_actionPerformed(e);
1253 followHighlightMenuItem.setVisible(true);
1254 followHighlightMenuItem.setState(true);
1255 followHighlightMenuItem.setText("Automatic Scrolling");
1256 followHighlightMenuItem.addActionListener(new ActionListener()
1259 public void actionPerformed(ActionEvent e)
1261 followHighlight_actionPerformed();
1266 modifyPID.setText("Modify Identity Threshold...");
1267 modifyPID.addActionListener(new java.awt.event.ActionListener()
1269 public void actionPerformed(ActionEvent e)
1271 modifyPID_actionPerformed(e);
1274 modifyConservation.setText("Modify Conservation Threshold...");
1276 .addActionListener(new java.awt.event.ActionListener()
1278 public void actionPerformed(ActionEvent e)
1280 modifyConservation_actionPerformed(e);
1283 sortByTreeMenu.setText("By Tree Order");
1284 sort.setText("Sort");
1285 sort.addMenuListener(new MenuListener()
1287 public void menuSelected(MenuEvent e)
1292 public void menuDeselected(MenuEvent e)
1296 public void menuCanceled(MenuEvent e)
1300 sortByAnnotScore.setText("by Score");
1301 sort.add(sortByAnnotScore);
1302 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1305 public void menuCanceled(MenuEvent e)
1309 public void menuDeselected(MenuEvent e)
1313 public void menuSelected(MenuEvent e)
1315 buildSortByAnnotationScoresMenu();
1318 sortByAnnotScore.setVisible(false);
1320 calculateTree.setText("Calculate Tree");
1322 jMenu2.setText("Export Image");
1323 padGapsMenuitem.setText("Pad Gaps");
1324 padGapsMenuitem.setState(jalview.bin.Cache
1325 .getDefault("PAD_GAPS", false));
1326 padGapsMenuitem.addActionListener(new ActionListener()
1328 public void actionPerformed(ActionEvent e)
1330 padGapsMenuitem_actionPerformed(e);
1333 vamsasStore.setVisible(false);
1334 vamsasStore.setText("VAMSAS store");
1335 vamsasStore.addActionListener(new ActionListener()
1337 public void actionPerformed(ActionEvent e)
1339 vamsasStore_actionPerformed(e);
1342 showTranslation.setText("Translate cDNA");
1343 showTranslation.addActionListener(new ActionListener()
1345 public void actionPerformed(ActionEvent e)
1347 showTranslation_actionPerformed(e);
1350 extractScores.setText("Extract Scores...");
1351 extractScores.addActionListener(new ActionListener()
1353 public void actionPerformed(ActionEvent e)
1355 extractScores_actionPerformed(e);
1358 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1360 showProducts.setText("Get Cross References");
1362 * showProducts.addActionListener(new ActionListener() {
1364 * public void actionPerformed(ActionEvent e) {
1365 * showProducts_actionPerformed(e); } });
1367 featureSettings.setText("Feature Settings...");
1368 featureSettings.addActionListener(new ActionListener()
1370 public void actionPerformed(ActionEvent e)
1372 featureSettings_actionPerformed(e);
1375 fetchSequence.setText("Fetch Sequence(s)...");
1376 fetchSequence.addActionListener(new ActionListener()
1378 public void actionPerformed(ActionEvent e)
1380 fetchSequence_actionPerformed(e);
1384 annotationColour.setText("By Annotation...");
1385 annotationColour.addActionListener(new ActionListener()
1387 public void actionPerformed(ActionEvent e)
1389 annotationColour_actionPerformed(e);
1392 associatedData.setText("Load Features / Annotations");
1393 associatedData.addActionListener(new ActionListener()
1395 public void actionPerformed(ActionEvent e)
1397 associatedData_actionPerformed(e);
1400 autoCalculate.setText("Autocalculate Consensus");
1401 autoCalculate.setState(jalview.bin.Cache.getDefault(
1402 "AUTO_CALC_CONSENSUS", true));
1403 autoCalculate.addActionListener(new ActionListener()
1405 public void actionPerformed(ActionEvent e)
1407 autoCalculate_actionPerformed(e);
1410 sortByTree.setText("Sort Alignment With New Tree");
1411 sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1412 sortByTree.setState(jalview.bin.Cache.getDefault(
1413 "SORT_BY_TREE", false));
1414 sortByTree.addActionListener(new ActionListener()
1416 public void actionPerformed(ActionEvent e)
1418 sortByTreeOption_actionPerformed(e);
1422 listenToViewSelections.setText("Listen for selections");
1423 listenToViewSelections.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1424 listenToViewSelections.setState(false);
1425 listenToViewSelections.addActionListener(new ActionListener()
1427 public void actionPerformed(ActionEvent e)
1429 listenToViewSelections_actionPerformed(e);
1433 addSequenceMenu.setText("Add Sequences");
1434 addFromFile.setText("From File");
1435 addFromFile.addActionListener(new ActionListener()
1437 public void actionPerformed(ActionEvent e)
1439 addFromFile_actionPerformed(e);
1442 addFromText.setText("From Textbox");
1443 addFromText.addActionListener(new ActionListener()
1445 public void actionPerformed(ActionEvent e)
1447 addFromText_actionPerformed(e);
1450 addFromURL.setText("From URL");
1451 addFromURL.addActionListener(new ActionListener()
1453 public void actionPerformed(ActionEvent e)
1455 addFromURL_actionPerformed(e);
1458 exportFeatures.setText("Export Features...");
1459 exportFeatures.addActionListener(new ActionListener()
1461 public void actionPerformed(ActionEvent e)
1463 exportFeatures_actionPerformed(e);
1466 exportAnnotations.setText("Export Annotations...");
1467 exportAnnotations.addActionListener(new ActionListener()
1469 public void actionPerformed(ActionEvent e)
1471 exportAnnotations_actionPerformed(e);
1474 statusPanel.setLayout(gridLayout1);
1475 jMenu3.setText("Show");
1476 showAllSeqs.setText("All Sequences");
1477 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1478 showAllSeqs.addActionListener(new ActionListener()
1480 public void actionPerformed(ActionEvent e)
1482 showAllSeqs_actionPerformed(e);
1485 showAllColumns.setText("All Columns");
1486 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1487 showAllColumns.addActionListener(new ActionListener()
1489 public void actionPerformed(ActionEvent e)
1491 showAllColumns_actionPerformed(e);
1494 hideMenu.setText("Hide");
1495 hideSelSequences.setText("Selected Sequences");
1496 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1497 hideSelSequences.addActionListener(new ActionListener()
1499 public void actionPerformed(ActionEvent e)
1501 hideSelSequences_actionPerformed(e);
1504 hideSelColumns.setText("Selected Columns");
1505 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1506 hideSelColumns.addActionListener(new ActionListener()
1508 public void actionPerformed(ActionEvent e)
1510 hideSelColumns_actionPerformed(e);
1513 hideAllSelection.setText("Selected Region");
1514 hideAllSelection.addActionListener(new ActionListener()
1516 public void actionPerformed(ActionEvent e)
1518 hideAllSelection_actionPerformed(e);
1521 // TODO: should be hidden if no selection exists.
1522 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1523 hideAllButSelection.addActionListener(new ActionListener()
1525 public void actionPerformed(ActionEvent e)
1527 hideAllButSelection_actionPerformed(e);
1530 showAllhidden.setText("All Sequences and Columns");
1532 .setToolTipText("H toggles visibility of hidden or selected regions.");
1533 showAllhidden.addActionListener(new ActionListener()
1535 public void actionPerformed(ActionEvent e)
1537 showAllhidden_actionPerformed(e);
1541 hiddenMarkers.setText("Show Hidden Markers");
1542 hiddenMarkers.addActionListener(new ActionListener()
1544 public void actionPerformed(ActionEvent e)
1546 hiddenMarkers_actionPerformed(e);
1549 invertColSel.setText("Invert Column Selection");
1550 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1551 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1552 .getMenuShortcutKeyMask()
1553 | java.awt.event.KeyEvent.ALT_MASK, false));
1554 invertColSel.addActionListener(new ActionListener()
1556 public void actionPerformed(ActionEvent e)
1558 invertColSel_actionPerformed(e);
1561 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1563 public void stateChanged(ChangeEvent evt)
1565 JTabbedPane pane = (JTabbedPane) evt.getSource();
1566 int sel = pane.getSelectedIndex();
1567 tabSelectionChanged(sel);
1570 tabbedPane.addMouseListener(new MouseAdapter()
1572 public void mousePressed(MouseEvent e)
1574 tabbedPane_mousePressed(e);
1577 tabbedPane.addFocusListener(new FocusAdapter()
1579 public void focusGained(FocusEvent e)
1581 tabbedPane_focusGained(e);
1584 save.setText("Save");
1585 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1586 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1587 .getMenuShortcutKeyMask(), false));
1588 save.addActionListener(new ActionListener()
1590 public void actionPerformed(ActionEvent e)
1592 save_actionPerformed(e);
1595 reload.setEnabled(false);
1596 reload.setText("Reload");
1597 reload.addActionListener(new ActionListener()
1599 public void actionPerformed(ActionEvent e)
1601 reload_actionPerformed(e);
1604 newView.setText("New View");
1605 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1606 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1607 .getMenuShortcutKeyMask(), false));
1608 newView.addActionListener(new ActionListener()
1610 public void actionPerformed(ActionEvent e)
1612 newView_actionPerformed(e);
1615 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1616 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1617 textColour.setText("Colour Text ...");
1618 textColour.addActionListener(new ActionListener()
1620 public void actionPerformed(ActionEvent e)
1622 textColour_actionPerformed(e);
1625 formatMenu.setText("Format");
1626 selectMenu.setText("Select");
1627 idRightAlign.setText("Right Align Sequence Id");
1628 idRightAlign.addActionListener(new ActionListener()
1630 public void actionPerformed(ActionEvent e)
1632 idRightAlign_actionPerformed(e);
1635 gatherViews.setEnabled(false);
1636 gatherViews.setText("Gather Views");
1637 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1638 java.awt.event.KeyEvent.VK_G, 0, false));
1639 gatherViews.addActionListener(new ActionListener()
1641 public void actionPerformed(ActionEvent e)
1643 gatherViews_actionPerformed(e);
1646 expandViews.setEnabled(false);
1647 expandViews.setText("Expand Views");
1648 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1649 java.awt.event.KeyEvent.VK_X, 0, false));
1650 expandViews.addActionListener(new ActionListener()
1652 public void actionPerformed(ActionEvent e)
1654 expandViews_actionPerformed(e);
1657 pageSetup.setText("Page Setup ...");
1658 pageSetup.addActionListener(new ActionListener()
1660 public void actionPerformed(ActionEvent e)
1662 pageSetup_actionPerformed(e);
1665 alignmentProperties.setText("Alignment Properties...");
1666 alignmentProperties.addActionListener(new ActionListener()
1668 public void actionPerformed(ActionEvent actionEvent)
1670 alignmentProperties();
1673 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1674 autoAnnMenu.setText("Autocalculated Annotation");
1675 alignFrameMenuBar.add(fileMenu);
1676 alignFrameMenuBar.add(editMenu);
1677 alignFrameMenuBar.add(selectMenu);
1678 alignFrameMenuBar.add(viewMenu);
1679 alignFrameMenuBar.add(formatMenu);
1680 alignFrameMenuBar.add(colourMenu);
1681 alignFrameMenuBar.add(calculateMenu);
1682 alignFrameMenuBar.add(webService);
1683 fileMenu.add(fetchSequence);
1684 fileMenu.add(addSequenceMenu);
1685 fileMenu.add(reload);
1686 fileMenu.addSeparator();
1687 fileMenu.add(vamsasStore);
1689 fileMenu.add(saveAs);
1690 fileMenu.add(outputTextboxMenu);
1691 fileMenu.add(pageSetup);
1692 fileMenu.add(printMenuItem);
1693 fileMenu.addSeparator();
1694 fileMenu.add(jMenu2);
1695 fileMenu.add(exportFeatures);
1696 fileMenu.add(exportAnnotations);
1697 fileMenu.add(LoadtreeMenuItem);
1698 fileMenu.add(associatedData);
1699 fileMenu.addSeparator();
1700 fileMenu.add(closeMenuItem);
1701 editMenu.add(undoMenuItem);
1702 editMenu.add(redoMenuItem);
1705 editMenu.add(pasteMenu);
1706 editMenu.add(delete);
1707 editMenu.addSeparator();
1708 editMenu.add(remove2LeftMenuItem);
1709 editMenu.add(remove2RightMenuItem);
1710 editMenu.add(removeGappedColumnMenuItem);
1711 editMenu.add(removeAllGapsMenuItem);
1712 editMenu.add(removeRedundancyMenuItem);
1713 editMenu.addSeparator();
1714 // dont add these yet in the CVS build - they cannot be undone!
1715 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1716 // editMenu.add(justifyLeftMenuItem);
1717 // editMenu.add(justifyRightMenuItem);
1718 // editMenu.addSeparator();
1719 editMenu.add(padGapsMenuitem);
1720 viewMenu.add(newView);
1721 viewMenu.add(expandViews);
1722 viewMenu.add(gatherViews);
1723 viewMenu.addSeparator();
1724 viewMenu.add(jMenu3);
1725 viewMenu.add(hideMenu);
1726 viewMenu.addSeparator();
1727 viewMenu.add(followHighlightMenuItem);
1728 viewMenu.add(annotationPanelMenuItem);
1729 autoAnnMenu.add(applyAutoAnnotationSettings);
1730 autoAnnMenu.add(showConsensusHistogram);
1731 autoAnnMenu.add(showSequenceLogo);
1732 autoAnnMenu.addSeparator();
1733 autoAnnMenu.add(showGroupConservation);
1734 autoAnnMenu.add(showGroupConsensus);
1735 viewMenu.add(autoAnnMenu);
1736 viewMenu.addSeparator();
1737 viewMenu.add(showSeqFeatures);
1738 // viewMenu.add(showSeqFeaturesHeight);
1740 viewMenu.add(featureSettings);
1741 tooltipSettingsMenu.add(showDbRefsMenuitem);
1742 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1743 viewMenu.add(tooltipSettingsMenu);
1744 viewMenu.addSeparator();
1745 viewMenu.add(alignmentProperties);
1746 viewMenu.addSeparator();
1747 viewMenu.add(overviewMenuItem);
1748 colourMenu.add(applyToAllGroups);
1749 colourMenu.add(textColour);
1750 colourMenu.addSeparator();
1751 colourMenu.add(noColourmenuItem);
1752 colourMenu.add(clustalColour);
1753 colourMenu.add(BLOSUM62Colour);
1754 colourMenu.add(PIDColour);
1755 colourMenu.add(zappoColour);
1756 colourMenu.add(taylorColour);
1757 colourMenu.add(hydrophobicityColour);
1758 colourMenu.add(helixColour);
1759 colourMenu.add(strandColour);
1760 colourMenu.add(turnColour);
1761 colourMenu.add(buriedColour);
1762 colourMenu.add(nucleotideColour);
1763 colourMenu.add(userDefinedColour);
1764 colourMenu.addSeparator();
1765 colourMenu.add(conservationMenuItem);
1766 colourMenu.add(modifyConservation);
1767 colourMenu.add(abovePIDThreshold);
1768 colourMenu.add(modifyPID);
1769 colourMenu.add(annotationColour);
1770 calculateMenu.add(sort);
1771 calculateMenu.add(calculateTree);
1772 calculateMenu.addSeparator();
1773 calculateMenu.add(pairwiseAlignmentMenuItem);
1774 calculateMenu.add(PCAMenuItem);
1775 calculateMenu.addSeparator();
1776 calculateMenu.add(showTranslation);
1777 calculateMenu.add(showProducts);
1778 calculateMenu.add(autoCalculate);
1779 calculateMenu.add(sortByTree);
1780 calculateMenu.addSeparator();
1781 calculateMenu.add(extractScores);
1782 webServiceNoServices = new JMenuItem("<No Services>");
1783 webService.add(webServiceNoServices);
1784 pasteMenu.add(pasteNew);
1785 pasteMenu.add(pasteThis);
1786 sort.add(sortIDMenuItem);
1787 sort.add(sortLengthMenuItem);
1788 sort.add(sortGroupMenuItem);
1789 sort.add(sortPairwiseMenuItem);
1790 sort.add(sortByTreeMenu);
1791 calculateTree.add(averageDistanceTreeMenuItem);
1792 calculateTree.add(neighbourTreeMenuItem);
1793 calculateTree.add(avDistanceTreeBlosumMenuItem);
1794 calculateTree.add(njTreeBlosumMenuItem);
1795 jMenu2.add(htmlMenuItem);
1796 jMenu2.add(epsFile);
1797 jMenu2.add(createPNG);
1798 addSequenceMenu.add(addFromFile);
1799 addSequenceMenu.add(addFromText);
1800 addSequenceMenu.add(addFromURL);
1801 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1802 statusPanel.add(statusBar, null);
1803 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1804 jMenu3.add(showAllColumns);
1805 jMenu3.add(showAllSeqs);
1806 jMenu3.add(showAllhidden);
1807 hideMenu.add(hideSelColumns);
1808 hideMenu.add(hideSelSequences);
1809 hideMenu.add(hideAllSelection);
1810 hideMenu.add(hideAllButSelection);
1812 formatMenu.add(font);
1813 formatMenu.addSeparator();
1814 formatMenu.add(wrapMenuItem);
1815 formatMenu.add(scaleAbove);
1816 formatMenu.add(scaleLeft);
1817 formatMenu.add(scaleRight);
1818 formatMenu.add(seqLimits);
1819 formatMenu.add(idRightAlign);
1820 formatMenu.add(hiddenMarkers);
1821 formatMenu.add(viewBoxesMenuItem);
1822 formatMenu.add(viewTextMenuItem);
1823 formatMenu.add(colourTextMenuItem);
1824 formatMenu.add(renderGapsMenuItem);
1825 formatMenu.add(centreColumnLabelsMenuItem);
1826 formatMenu.add(showNonconservedMenuItem);
1827 selectMenu.add(findMenuItem);
1828 selectMenu.addSeparator();
1829 selectMenu.add(selectAllSequenceMenuItem);
1830 selectMenu.add(deselectAllSequenceMenuItem);
1831 selectMenu.add(invertSequenceMenuItem);
1832 selectMenu.add(invertColSel);
1833 selectMenu.add(deleteGroups);
1834 selectMenu.add(grpsFromSelection);
1835 // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
1836 //selectMenu.addSeparator();
1837 //selectMenu.add(listenToViewSelections);
1840 protected void listenToViewSelections_actionPerformed(ActionEvent e)
1842 // TODO Auto-generated method stub
1846 protected void showAllhidden_actionPerformed(ActionEvent e)
1848 // TODO Auto-generated method stub
1852 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1854 // TODO Auto-generated method stub
1858 protected void hideAllSelection_actionPerformed(ActionEvent e)
1860 // TODO Auto-generated method stub
1864 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1866 // TODO Auto-generated method stub
1870 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1872 // TODO Auto-generated method stub
1876 protected void showSequenceLogo_actionPerformed(ActionEvent e)
1878 // TODO Auto-generated method stub
1882 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1884 // TODO Auto-generated method stub
1888 protected void showGroupConsensus_actionPerformed(ActionEvent e)
1890 // TODO Auto-generated method stub
1894 protected void showGroupConservation_actionPerformed(ActionEvent e)
1896 // TODO Auto-generated method stub
1900 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1902 // TODO Auto-generated method stub
1906 protected void showSeqFeaturesHeight_actionPerformed(
1907 ActionEvent actionEvent)
1909 // TODO Auto-generated method stub
1913 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1915 // TODO Auto-generated method stub
1919 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1921 // TODO Auto-generated method stub
1925 protected void followHighlight_actionPerformed()
1927 // TODO Auto-generated method stub
1931 protected void showNpFeats_actionPerformed(ActionEvent e)
1933 // TODO Auto-generated method stub
1937 protected void showDbRefs_actionPerformed(ActionEvent e)
1939 // TODO Auto-generated method stub
1943 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1947 protected void showProducts_actionPerformed(ActionEvent e)
1951 protected void buildSortByAnnotationScoresMenu()
1955 protected void extractScores_actionPerformed(ActionEvent e)
1959 protected void outputText_actionPerformed(ActionEvent e)
1963 public void addFromFile_actionPerformed(ActionEvent e)
1968 public void addFromText_actionPerformed(ActionEvent e)
1973 public void addFromURL_actionPerformed(ActionEvent e)
1978 public void exportFeatures_actionPerformed(ActionEvent e)
1983 public void exportAnnotations_actionPerformed(ActionEvent e)
1988 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1992 protected void closeMenuItem_actionPerformed(boolean b)
1996 protected void redoMenuItem_actionPerformed(ActionEvent e)
2000 protected void undoMenuItem_actionPerformed(ActionEvent e)
2004 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2008 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2012 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2016 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2020 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2024 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2028 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2032 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2036 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2040 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2044 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2048 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2052 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2056 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2060 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2064 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2068 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2072 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2076 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2080 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2084 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2088 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2092 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2096 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2100 protected void clustalColour_actionPerformed(ActionEvent e)
2104 protected void zappoColour_actionPerformed(ActionEvent e)
2108 protected void taylorColour_actionPerformed(ActionEvent e)
2112 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2116 protected void helixColour_actionPerformed(ActionEvent e)
2120 protected void strandColour_actionPerformed(ActionEvent e)
2124 protected void turnColour_actionPerformed(ActionEvent e)
2128 protected void buriedColour_actionPerformed(ActionEvent e)
2132 protected void userDefinedColour_actionPerformed(ActionEvent e)
2136 protected void PIDColour_actionPerformed(ActionEvent e)
2140 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2144 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2148 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2152 protected void printMenuItem_actionPerformed(ActionEvent e)
2156 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2160 protected void findMenuItem_actionPerformed(ActionEvent e)
2164 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2168 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2172 protected void nucleotideColour_actionPerformed(ActionEvent e)
2176 protected void deleteGroups_actionPerformed(ActionEvent e)
2180 protected void copy_actionPerformed(ActionEvent e)
2184 protected void cut_actionPerformed(ActionEvent e)
2188 protected void delete_actionPerformed(ActionEvent e)
2192 protected void pasteNew_actionPerformed(ActionEvent e)
2196 protected void pasteThis_actionPerformed(ActionEvent e)
2200 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2204 public void createPNG(java.io.File f)
2208 protected void font_actionPerformed(ActionEvent e)
2212 protected void seqLimit_actionPerformed(ActionEvent e)
2216 public void seqDBRef_actionPerformed(ActionEvent e)
2221 public void createEPS(java.io.File f)
2225 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2229 protected void jpred_actionPerformed(ActionEvent e)
2233 protected void scaleAbove_actionPerformed(ActionEvent e)
2237 protected void scaleLeft_actionPerformed(ActionEvent e)
2241 protected void scaleRight_actionPerformed(ActionEvent e)
2245 protected void modifyPID_actionPerformed(ActionEvent e)
2249 protected void modifyConservation_actionPerformed(ActionEvent e)
2253 protected void saveAs_actionPerformed(ActionEvent e)
2257 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2261 public void vamsasStore_actionPerformed(ActionEvent e)
2266 public void vamsasLoad_actionPerformed(ActionEvent e)
2271 public void showTranslation_actionPerformed(ActionEvent e)
2276 public void featureSettings_actionPerformed(ActionEvent e)
2281 public void fetchSequence_actionPerformed(ActionEvent e)
2286 public void smoothFont_actionPerformed(ActionEvent e)
2291 public void annotationColour_actionPerformed(ActionEvent e)
2296 public void associatedData_actionPerformed(ActionEvent e)
2301 public void autoCalculate_actionPerformed(ActionEvent e)
2306 public void sortByTreeOption_actionPerformed(ActionEvent e)
2311 public void showAllSeqs_actionPerformed(ActionEvent e)
2316 public void showAllColumns_actionPerformed(ActionEvent e)
2321 public void hideSelSequences_actionPerformed(ActionEvent e)
2326 public void hideSelColumns_actionPerformed(ActionEvent e)
2331 public void hiddenMarkers_actionPerformed(ActionEvent e)
2336 public void findPdbId_actionPerformed(ActionEvent e)
2341 public void enterPdbId_actionPerformed(ActionEvent e)
2346 public void pdbFile_actionPerformed(ActionEvent e)
2351 public void invertColSel_actionPerformed(ActionEvent e)
2356 public void tabSelectionChanged(int sel)
2361 public void tabbedPane_mousePressed(MouseEvent e)
2366 public void tabbedPane_focusGained(FocusEvent e)
2371 public void save_actionPerformed(ActionEvent e)
2376 public void reload_actionPerformed(ActionEvent e)
2381 public void newView_actionPerformed(ActionEvent e)
2386 public void textColour_actionPerformed(ActionEvent e)
2391 public void idRightAlign_actionPerformed(ActionEvent e)
2396 public void expandViews_actionPerformed(ActionEvent e)
2401 public void gatherViews_actionPerformed(ActionEvent e)
2406 public void buildTreeMenu()
2411 public void pageSetup_actionPerformed(ActionEvent e)
2416 public void alignmentProperties()