2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.jbgui;
22 import java.awt.event.*;
25 import javax.swing.event.*;
27 import jalview.schemes.*;
29 public class GAlignFrame extends JInternalFrame
31 protected JMenuBar alignFrameMenuBar = new JMenuBar();
33 protected JMenu fileMenu = new JMenu();
35 protected JMenuItem closeMenuItem = new JMenuItem();
37 protected JMenu editMenu = new JMenu();
39 protected JMenu viewMenu = new JMenu();
41 protected JMenu colourMenu = new JMenu();
43 protected JMenu calculateMenu = new JMenu();
45 protected JMenu webService = new JMenu();
47 protected JMenuItem webServiceNoServices;
49 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
51 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
53 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
55 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
57 protected JMenuItem remove2RightMenuItem = new JMenuItem();
59 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
61 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
63 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
65 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
67 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
69 protected JMenuItem sortIDMenuItem = new JMenuItem();
71 protected JMenuItem sortLengthMenuItem = new JMenuItem();
73 protected JMenuItem sortGroupMenuItem = new JMenuItem();
75 protected JMenu sortByAnnotScore = new JMenu();
77 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
79 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
81 protected JMenuItem PCAMenuItem = new JMenuItem();
83 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
85 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
87 BorderLayout borderLayout1 = new BorderLayout();
89 public JLabel statusBar = new JLabel();
91 protected JMenuItem saveAs = new JMenuItem();
93 protected JMenu outputTextboxMenu = new JMenu();
95 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
97 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
99 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
101 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
103 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
105 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
107 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
109 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
111 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
113 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
115 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
117 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
119 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
121 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
123 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
125 public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
127 JMenuItem htmlMenuItem = new JMenuItem();
129 JMenuItem overviewMenuItem = new JMenuItem();
131 protected JMenuItem undoMenuItem = new JMenuItem();
133 protected JMenuItem redoMenuItem = new JMenuItem();
135 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
137 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
139 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
141 JMenuItem printMenuItem = new JMenuItem();
143 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
145 JMenuItem findMenuItem = new JMenuItem();
147 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
149 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
150 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
152 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
154 JMenuItem deleteGroups = new JMenuItem();
156 JMenuItem delete = new JMenuItem();
158 JMenuItem copy = new JMenuItem();
160 JMenuItem cut = new JMenuItem();
162 JMenu pasteMenu = new JMenu();
164 JMenuItem pasteNew = new JMenuItem();
166 JMenuItem pasteThis = new JMenuItem();
168 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
170 JMenuItem createPNG = new JMenuItem();
172 protected JMenuItem font = new JMenuItem();
174 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
176 JMenuItem epsFile = new JMenuItem();
178 JMenuItem LoadtreeMenuItem = new JMenuItem();
180 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
182 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
184 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
186 protected JMenuItem modifyPID = new JMenuItem();
188 protected JMenuItem modifyConservation = new JMenuItem();
190 protected JMenu sortByTreeMenu = new JMenu();
192 protected JMenu sort = new JMenu();
194 protected JMenu calculateTree = new JMenu();
196 JMenu jMenu2 = new JMenu();
198 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
199 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
200 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
202 protected ButtonGroup colours = new ButtonGroup();
204 JMenuItem vamsasStore = new JMenuItem();
206 protected JMenuItem showTranslation = new JMenuItem();
208 protected JMenuItem extractScores = new JMenuItem();
210 protected JMenu showProducts = new JMenu();
212 public JMenuItem featureSettings = new JMenuItem();
214 JMenuItem fetchSequence = new JMenuItem();
216 JMenuItem annotationColour = new JMenuItem();
218 JMenuItem associatedData = new JMenuItem();
220 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
222 JMenu addSequenceMenu = new JMenu();
224 JMenuItem addFromFile = new JMenuItem();
226 JMenuItem addFromText = new JMenuItem();
228 JMenuItem addFromURL = new JMenuItem();
230 JMenuItem exportAnnotations = new JMenuItem();
232 JMenuItem exportFeatures = new JMenuItem();
234 protected JPanel statusPanel = new JPanel();
236 GridLayout gridLayout1 = new GridLayout();
238 JMenu jMenu3 = new JMenu();
240 JMenuItem showAllSeqs = new JMenuItem();
242 JMenuItem showAllColumns = new JMenuItem();
244 JMenu hideMenu = new JMenu();
246 JMenuItem hideSelSequences = new JMenuItem();
248 JMenuItem hideSelColumns = new JMenuItem();
250 JMenuItem hideAllButSelection = new JMenuItem();
252 JMenuItem hideAllSelection = new JMenuItem();
254 JMenuItem showAllhidden = new JMenuItem();
256 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
258 JMenuItem invertColSel = new JMenuItem();
260 protected JTabbedPane tabbedPane = new JTabbedPane();
262 JMenuItem save = new JMenuItem();
264 protected JMenuItem reload = new JMenuItem();
266 JMenuItem newView = new JMenuItem();
268 JMenuItem textColour = new JMenuItem();
270 JMenu formatMenu = new JMenu();
272 JMenu selectMenu = new JMenu();
274 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
276 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
278 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
280 protected JMenuItem gatherViews = new JMenuItem();
282 protected JMenuItem expandViews = new JMenuItem();
284 JMenuItem pageSetup = new JMenuItem();
286 JMenuItem alignmentProperties = new JMenuItem();
288 JMenu tooltipSettingsMenu = new JMenu();
290 private JMenuItem justifyLeftMenuItem=new JMenuItem();
292 private JMenuItem justifyRightMenuItem=new JMenuItem();
294 JMenu autoAnnMenu = new JMenu();
295 protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
296 protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
297 protected JCheckBoxMenuItem showConsensusHistogram=new JCheckBoxMenuItem();
298 protected JCheckBoxMenuItem showSequenceLogo=new JCheckBoxMenuItem();
299 protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem();
301 private JMenuItem grpsFromSelection = new JMenuItem();
307 setJMenuBar(alignFrameMenuBar);
309 // dynamically fill save as menu with available formats
310 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
312 JMenuItem item = new JMenuItem(
313 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
315 item.addActionListener(new java.awt.event.ActionListener()
317 public void actionPerformed(ActionEvent e)
319 outputText_actionPerformed(e);
323 outputTextboxMenu.add(item);
325 } catch (Exception e)
329 if (!new jalview.util.Platform().isAMac())
331 closeMenuItem.setMnemonic('C');
332 outputTextboxMenu.setMnemonic('T');
333 undoMenuItem.setMnemonic('Z');
334 redoMenuItem.setMnemonic('0');
335 copy.setMnemonic('C');
336 cut.setMnemonic('U');
337 pasteMenu.setMnemonic('P');
338 reload.setMnemonic('R');
341 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
343 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
344 .getUserColourSchemes().keys();
346 while (userColours.hasMoreElements())
348 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
349 userColours.nextElement().toString());
350 radioItem.setName("USER_DEFINED");
351 radioItem.addMouseListener(new MouseAdapter()
353 public void mousePressed(MouseEvent evt)
355 if (evt.isControlDown()
356 || SwingUtilities.isRightMouseButton(evt))
359 .removeActionListener(radioItem.getActionListeners()[0]);
361 int option = JOptionPane.showInternalConfirmDialog(
362 jalview.gui.Desktop.desktop,
363 "Remove from default list?",
364 "Remove user defined colour",
365 JOptionPane.YES_NO_OPTION);
366 if (option == JOptionPane.YES_OPTION)
368 jalview.gui.UserDefinedColours
369 .removeColourFromDefaults(radioItem.getText());
370 colourMenu.remove(radioItem);
374 radioItem.addActionListener(new ActionListener()
376 public void actionPerformed(ActionEvent evt)
378 userDefinedColour_actionPerformed(evt);
385 radioItem.addActionListener(new ActionListener()
387 public void actionPerformed(ActionEvent evt)
389 userDefinedColour_actionPerformed(evt);
392 colourMenu.insert(radioItem, 15);
393 colours.add(radioItem);
396 colours.add(noColourmenuItem);
397 colours.add(clustalColour);
398 colours.add(zappoColour);
399 colours.add(taylorColour);
400 colours.add(hydrophobicityColour);
401 colours.add(helixColour);
402 colours.add(strandColour);
403 colours.add(turnColour);
404 colours.add(buriedColour);
405 colours.add(userDefinedColour);
406 colours.add(PIDColour);
407 colours.add(BLOSUM62Colour);
408 colours.add(nucleotideColour);
410 setColourSelected(jalview.bin.Cache
411 .getDefault("DEFAULT_COLOUR", "None"));
415 public void setColourSelected(String defaultColour)
418 if (defaultColour != null)
420 int index = ColourSchemeProperty
421 .getColourIndexFromName(defaultColour);
425 case ColourSchemeProperty.NONE:
426 noColourmenuItem.setSelected(true);
428 case ColourSchemeProperty.CLUSTAL:
429 clustalColour.setSelected(true);
433 case ColourSchemeProperty.BLOSUM:
434 BLOSUM62Colour.setSelected(true);
438 case ColourSchemeProperty.PID:
439 PIDColour.setSelected(true);
443 case ColourSchemeProperty.ZAPPO:
444 zappoColour.setSelected(true);
448 case ColourSchemeProperty.TAYLOR:
449 taylorColour.setSelected(true);
452 case ColourSchemeProperty.HYDROPHOBIC:
453 hydrophobicityColour.setSelected(true);
457 case ColourSchemeProperty.HELIX:
458 helixColour.setSelected(true);
462 case ColourSchemeProperty.STRAND:
463 strandColour.setSelected(true);
467 case ColourSchemeProperty.TURN:
468 turnColour.setSelected(true);
472 case ColourSchemeProperty.BURIED:
473 buriedColour.setSelected(true);
477 case ColourSchemeProperty.NUCLEOTIDE:
478 nucleotideColour.setSelected(true);
482 case ColourSchemeProperty.USER_DEFINED:
483 userDefinedColour.setSelected(true);
491 private void jbInit() throws Exception
493 fileMenu.setText("File");
494 saveAs.setText("Save As...");
495 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
496 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
497 .getMenuShortcutKeyMask()
498 | java.awt.event.KeyEvent.SHIFT_MASK, false));
499 saveAs.addActionListener(new ActionListener()
501 public void actionPerformed(ActionEvent e)
503 saveAs_actionPerformed(e);
506 closeMenuItem.setText("Close");
507 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
508 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
509 .getMenuShortcutKeyMask(), false));
510 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
512 public void actionPerformed(ActionEvent e)
514 closeMenuItem_actionPerformed(false);
517 editMenu.setText("Edit");
518 viewMenu.setText("View");
519 colourMenu.setText("Colour");
520 calculateMenu.setText("Calculate");
521 webService.setText("Web Service");
522 selectAllSequenceMenuItem.setText("Select All");
523 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
524 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
525 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
526 selectAllSequenceMenuItem
527 .addActionListener(new java.awt.event.ActionListener()
529 public void actionPerformed(ActionEvent e)
531 selectAllSequenceMenuItem_actionPerformed(e);
534 deselectAllSequenceMenuItem.setText("Deselect All");
535 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
536 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
537 deselectAllSequenceMenuItem
538 .addActionListener(new java.awt.event.ActionListener()
540 public void actionPerformed(ActionEvent e)
542 deselectAllSequenceMenuItem_actionPerformed(e);
545 invertSequenceMenuItem.setText("Invert Sequence Selection");
546 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
547 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
548 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
549 invertSequenceMenuItem
550 .addActionListener(new java.awt.event.ActionListener()
552 public void actionPerformed(ActionEvent e)
554 invertSequenceMenuItem_actionPerformed(e);
557 grpsFromSelection.setText("Make Groups for selection");
558 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
560 public void actionPerformed(ActionEvent e)
562 makeGrpsFromSelection_actionPerformed(e);
566 remove2LeftMenuItem.setText("Remove Left");
567 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
568 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
569 .getMenuShortcutKeyMask(), false));
571 .addActionListener(new java.awt.event.ActionListener()
573 public void actionPerformed(ActionEvent e)
575 remove2LeftMenuItem_actionPerformed(e);
578 remove2RightMenuItem.setText("Remove Right");
579 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
580 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
581 .getMenuShortcutKeyMask(), false));
583 .addActionListener(new java.awt.event.ActionListener()
585 public void actionPerformed(ActionEvent e)
587 remove2RightMenuItem_actionPerformed(e);
590 removeGappedColumnMenuItem.setText("Remove Empty Columns");
591 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
592 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
593 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
594 removeGappedColumnMenuItem
595 .addActionListener(new java.awt.event.ActionListener()
597 public void actionPerformed(ActionEvent e)
599 removeGappedColumnMenuItem_actionPerformed(e);
602 removeAllGapsMenuItem.setText("Remove All Gaps");
603 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
604 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
605 .getDefaultToolkit().getMenuShortcutKeyMask()
606 | java.awt.event.KeyEvent.SHIFT_MASK, false));
607 removeAllGapsMenuItem
608 .addActionListener(new java.awt.event.ActionListener()
610 public void actionPerformed(ActionEvent e)
612 removeAllGapsMenuItem_actionPerformed(e);
615 justifyLeftMenuItem.setText("Left Justify Alignment");
616 justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
618 public void actionPerformed(ActionEvent e)
620 justifyLeftMenuItem_actionPerformed(e);
623 justifyRightMenuItem.setText("Right Justify Alignment");
624 justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
626 public void actionPerformed(ActionEvent e)
628 justifyRightMenuItem_actionPerformed(e);
631 viewBoxesMenuItem.setText("Boxes");
632 viewBoxesMenuItem.setState(true);
633 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
635 public void actionPerformed(ActionEvent e)
637 viewBoxesMenuItem_actionPerformed(e);
640 viewTextMenuItem.setText("Text");
641 viewTextMenuItem.setState(true);
642 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
644 public void actionPerformed(ActionEvent e)
646 viewTextMenuItem_actionPerformed(e);
649 showUnconservedMenuItem.setText("Show Unconserved");
650 showUnconservedMenuItem.setState(false);
651 showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
653 public void actionPerformed(ActionEvent e)
655 showUnconservedMenuItem_actionPerformed(e);
658 sortPairwiseMenuItem.setText("by Pairwise Identity");
660 .addActionListener(new java.awt.event.ActionListener()
662 public void actionPerformed(ActionEvent e)
664 sortPairwiseMenuItem_actionPerformed(e);
667 sortIDMenuItem.setText("by ID");
668 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
670 public void actionPerformed(ActionEvent e)
672 sortIDMenuItem_actionPerformed(e);
675 sortLengthMenuItem.setText("By Length");
676 sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
678 public void actionPerformed(ActionEvent e)
680 sortLengthMenuItem_actionPerformed(e);
683 sortGroupMenuItem.setText("by Group");
684 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
686 public void actionPerformed(ActionEvent e)
688 sortGroupMenuItem_actionPerformed(e);
691 removeRedundancyMenuItem.setText("Remove Redundancy...");
692 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
693 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
694 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
695 removeRedundancyMenuItem
696 .addActionListener(new java.awt.event.ActionListener()
698 public void actionPerformed(ActionEvent e)
700 removeRedundancyMenuItem_actionPerformed(e);
703 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
704 pairwiseAlignmentMenuItem
705 .addActionListener(new java.awt.event.ActionListener()
707 public void actionPerformed(ActionEvent e)
709 pairwiseAlignmentMenuItem_actionPerformed(e);
712 PCAMenuItem.setText("Principal Component Analysis");
713 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
715 public void actionPerformed(ActionEvent e)
717 PCAMenuItem_actionPerformed(e);
720 averageDistanceTreeMenuItem
721 .setText("Average Distance Using % Identity");
722 averageDistanceTreeMenuItem
723 .addActionListener(new java.awt.event.ActionListener()
725 public void actionPerformed(ActionEvent e)
727 averageDistanceTreeMenuItem_actionPerformed(e);
730 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
731 neighbourTreeMenuItem
732 .addActionListener(new java.awt.event.ActionListener()
734 public void actionPerformed(ActionEvent e)
736 neighbourTreeMenuItem_actionPerformed(e);
739 this.getContentPane().setLayout(borderLayout1);
740 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
741 statusBar.setBackground(Color.white);
742 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
743 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
744 statusBar.setText("Status bar");
745 outputTextboxMenu.setText("Output to Textbox");
746 clustalColour.setText("Clustalx");
748 clustalColour.addActionListener(new java.awt.event.ActionListener()
750 public void actionPerformed(ActionEvent e)
752 clustalColour_actionPerformed(e);
755 zappoColour.setText("Zappo");
756 zappoColour.addActionListener(new java.awt.event.ActionListener()
758 public void actionPerformed(ActionEvent e)
760 zappoColour_actionPerformed(e);
763 taylorColour.setText("Taylor");
764 taylorColour.addActionListener(new java.awt.event.ActionListener()
766 public void actionPerformed(ActionEvent e)
768 taylorColour_actionPerformed(e);
771 hydrophobicityColour.setText("Hydrophobicity");
773 .addActionListener(new java.awt.event.ActionListener()
775 public void actionPerformed(ActionEvent e)
777 hydrophobicityColour_actionPerformed(e);
780 helixColour.setText("Helix Propensity");
781 helixColour.addActionListener(new java.awt.event.ActionListener()
783 public void actionPerformed(ActionEvent e)
785 helixColour_actionPerformed(e);
788 strandColour.setText("Strand Propensity");
789 strandColour.addActionListener(new java.awt.event.ActionListener()
791 public void actionPerformed(ActionEvent e)
793 strandColour_actionPerformed(e);
796 turnColour.setText("Turn Propensity");
797 turnColour.addActionListener(new java.awt.event.ActionListener()
799 public void actionPerformed(ActionEvent e)
801 turnColour_actionPerformed(e);
804 buriedColour.setText("Buried Index");
805 buriedColour.addActionListener(new java.awt.event.ActionListener()
807 public void actionPerformed(ActionEvent e)
809 buriedColour_actionPerformed(e);
812 userDefinedColour.setText("User Defined...");
813 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
815 public void actionPerformed(ActionEvent e)
817 userDefinedColour_actionPerformed(e);
820 PIDColour.setText("Percentage Identity");
821 PIDColour.addActionListener(new java.awt.event.ActionListener()
823 public void actionPerformed(ActionEvent e)
825 PIDColour_actionPerformed(e);
828 BLOSUM62Colour.setText("BLOSUM62 Score");
829 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
831 public void actionPerformed(ActionEvent e)
833 BLOSUM62Colour_actionPerformed(e);
836 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
837 avDistanceTreeBlosumMenuItem
838 .addActionListener(new java.awt.event.ActionListener()
840 public void actionPerformed(ActionEvent e)
842 avTreeBlosumMenuItem_actionPerformed(e);
845 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
847 .addActionListener(new java.awt.event.ActionListener()
849 public void actionPerformed(ActionEvent e)
851 njTreeBlosumMenuItem_actionPerformed(e);
854 annotationPanelMenuItem.setActionCommand("");
855 annotationPanelMenuItem.setText("Show Annotations");
856 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
857 "SHOW_ANNOTATIONS", true));
858 annotationPanelMenuItem
859 .addActionListener(new java.awt.event.ActionListener()
861 public void actionPerformed(ActionEvent e)
863 annotationPanelMenuItem_actionPerformed(e);
866 colourTextMenuItem.setText("Colour Text");
868 .addActionListener(new java.awt.event.ActionListener()
870 public void actionPerformed(ActionEvent e)
872 colourTextMenuItem_actionPerformed(e);
875 htmlMenuItem.setText("HTML");
876 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
878 public void actionPerformed(ActionEvent e)
880 htmlMenuItem_actionPerformed(e);
883 overviewMenuItem.setText("Overview Window");
884 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
886 public void actionPerformed(ActionEvent e)
888 overviewMenuItem_actionPerformed(e);
891 undoMenuItem.setEnabled(false);
892 undoMenuItem.setText("Undo");
893 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
894 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
895 .getMenuShortcutKeyMask(), false));
896 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
898 public void actionPerformed(ActionEvent e)
900 undoMenuItem_actionPerformed(e);
903 redoMenuItem.setEnabled(false);
904 redoMenuItem.setText("Redo");
905 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
906 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
907 .getMenuShortcutKeyMask(), false));
908 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
910 public void actionPerformed(ActionEvent e)
912 redoMenuItem_actionPerformed(e);
915 conservationMenuItem.setText("By Conservation");
917 .addActionListener(new java.awt.event.ActionListener()
919 public void actionPerformed(ActionEvent e)
921 conservationMenuItem_actionPerformed(e);
924 noColourmenuItem.setText("None");
925 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
927 public void actionPerformed(ActionEvent e)
929 noColourmenuItem_actionPerformed(e);
932 wrapMenuItem.setText("Wrap");
933 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
935 public void actionPerformed(ActionEvent e)
937 wrapMenuItem_actionPerformed(e);
940 printMenuItem.setText("Print ...");
941 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
942 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
943 .getMenuShortcutKeyMask(), false));
944 printMenuItem.addActionListener(new java.awt.event.ActionListener()
946 public void actionPerformed(ActionEvent e)
948 printMenuItem_actionPerformed(e);
951 renderGapsMenuItem.setText("Show Gaps");
952 renderGapsMenuItem.setState(true);
954 .addActionListener(new java.awt.event.ActionListener()
956 public void actionPerformed(ActionEvent e)
958 renderGapsMenuItem_actionPerformed(e);
961 findMenuItem.setText("Find...");
962 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
963 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
964 .getMenuShortcutKeyMask(), false));
965 findMenuItem.addActionListener(new java.awt.event.ActionListener()
967 public void actionPerformed(ActionEvent e)
969 findMenuItem_actionPerformed(e);
972 abovePIDThreshold.setText("Above Identity Threshold");
973 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
975 public void actionPerformed(ActionEvent e)
977 abovePIDThreshold_actionPerformed(e);
980 showSeqFeatures.setText("Show Sequence Features");
981 showSeqFeatures.addActionListener(new ActionListener()
983 public void actionPerformed(ActionEvent actionEvent)
985 showSeqFeatures_actionPerformed(actionEvent);
989 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
990 showSeqFeaturesHeight.addActionListener(new ActionListener()
992 public void actionPerformed(ActionEvent actionEvent)
994 showSeqFeaturesHeight_actionPerformed(actionEvent);
997 showDbRefsMenuitem.setText("Show Database Refs");
998 showDbRefsMenuitem.addActionListener(new ActionListener()
1001 public void actionPerformed(ActionEvent e)
1003 showDbRefs_actionPerformed(e);
1007 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1008 showNpFeatsMenuitem.addActionListener(new ActionListener()
1011 public void actionPerformed(ActionEvent e)
1013 showNpFeats_actionPerformed(e);
1017 showGroupConservation.setText("Group Conservation");
1018 showGroupConservation.addActionListener(new ActionListener()
1021 public void actionPerformed(ActionEvent e)
1023 showGroupConservation_actionPerformed(e);
1028 showGroupConsensus.setText("Group Consensus");
1029 showGroupConsensus.addActionListener(new ActionListener()
1032 public void actionPerformed(ActionEvent e)
1034 showGroupConsensus_actionPerformed(e);
1038 showConsensusHistogram.setText("Show Consensus Histogram");
1039 showConsensusHistogram.addActionListener(new ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 showConsensusHistogram_actionPerformed(e);
1048 showSequenceLogo.setText("Show Consensus Logo");
1049 showSequenceLogo.addActionListener(new ActionListener()
1052 public void actionPerformed(ActionEvent e)
1054 showSequenceLogo_actionPerformed(e);
1058 applyAutoAnnotationSettings.setText("Apply to all groups");
1059 applyAutoAnnotationSettings.setState(false);
1060 applyAutoAnnotationSettings.setVisible(true);
1061 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1064 public void actionPerformed(ActionEvent e)
1066 applyAutoAnnotationSettings_actionPerformed(e);
1071 nucleotideColour.setText("Nucleotide");
1072 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1074 public void actionPerformed(ActionEvent e)
1076 nucleotideColour_actionPerformed(e);
1079 deleteGroups.setText("Undefine groups");
1080 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1081 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1082 .getMenuShortcutKeyMask(), false));
1083 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1085 public void actionPerformed(ActionEvent e)
1087 deleteGroups_actionPerformed(e);
1090 copy.setText("Copy");
1091 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1092 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1093 .getMenuShortcutKeyMask(), false));
1095 copy.addActionListener(new java.awt.event.ActionListener()
1097 public void actionPerformed(ActionEvent e)
1099 copy_actionPerformed(e);
1103 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1104 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1105 .getMenuShortcutKeyMask(), false));
1106 cut.addActionListener(new java.awt.event.ActionListener()
1108 public void actionPerformed(ActionEvent e)
1110 cut_actionPerformed(e);
1113 delete.setText("Delete");
1114 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1115 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1116 delete.addActionListener(new java.awt.event.ActionListener()
1118 public void actionPerformed(ActionEvent e)
1120 delete_actionPerformed(e);
1123 pasteMenu.setText("Paste");
1124 pasteNew.setText("To New Alignment");
1125 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1126 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1127 .getMenuShortcutKeyMask()
1128 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1129 pasteNew.addActionListener(new java.awt.event.ActionListener()
1131 public void actionPerformed(ActionEvent e)
1133 pasteNew_actionPerformed(e);
1136 pasteThis.setText("Add To This Alignment");
1137 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1138 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1139 .getMenuShortcutKeyMask(), false));
1140 pasteThis.addActionListener(new java.awt.event.ActionListener()
1142 public void actionPerformed(ActionEvent e)
1144 pasteThis_actionPerformed(e);
1147 applyToAllGroups.setText("Apply Colour To All Groups");
1148 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1150 public void actionPerformed(ActionEvent e)
1152 applyToAllGroups_actionPerformed(e);
1155 createPNG.addActionListener(new java.awt.event.ActionListener()
1157 public void actionPerformed(ActionEvent e)
1162 createPNG.setActionCommand("Save As PNG Image");
1163 createPNG.setText("PNG");
1164 font.setText("Font...");
1165 font.addActionListener(new java.awt.event.ActionListener()
1167 public void actionPerformed(ActionEvent e)
1169 font_actionPerformed(e);
1173 seqLimits.setText("Show Sequence Limits");
1174 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1175 seqLimits.addActionListener(new java.awt.event.ActionListener()
1177 public void actionPerformed(ActionEvent e)
1179 seqLimit_actionPerformed(e);
1182 epsFile.setText("EPS");
1183 epsFile.addActionListener(new java.awt.event.ActionListener()
1185 public void actionPerformed(ActionEvent e)
1190 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1191 LoadtreeMenuItem.setText("Load Associated Tree");
1192 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1194 public void actionPerformed(ActionEvent e)
1196 LoadtreeMenuItem_actionPerformed(e);
1199 scaleAbove.setVisible(false);
1200 scaleAbove.setText("Scale Above");
1201 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1203 public void actionPerformed(ActionEvent e)
1205 scaleAbove_actionPerformed(e);
1208 scaleLeft.setVisible(false);
1209 scaleLeft.setSelected(true);
1210 scaleLeft.setText("Scale Left");
1211 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1213 public void actionPerformed(ActionEvent e)
1215 scaleLeft_actionPerformed(e);
1218 scaleRight.setVisible(false);
1219 scaleRight.setSelected(true);
1220 scaleRight.setText("Scale Right");
1221 scaleRight.addActionListener(new java.awt.event.ActionListener()
1223 public void actionPerformed(ActionEvent e)
1225 scaleRight_actionPerformed(e);
1228 centreColumnLabelsMenuItem.setVisible(true);
1229 centreColumnLabelsMenuItem.setState(false);
1230 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1231 centreColumnLabelsMenuItem
1232 .addActionListener(new java.awt.event.ActionListener()
1234 public void actionPerformed(ActionEvent e)
1236 centreColumnLabels_actionPerformed(e);
1239 followHighlightMenuItem.setVisible(true);
1240 followHighlightMenuItem.setState(true);
1241 followHighlightMenuItem.setText("Automatic Scrolling");
1242 followHighlightMenuItem.addActionListener(new ActionListener()
1245 public void actionPerformed(ActionEvent e)
1247 followHighlight_actionPerformed();
1252 modifyPID.setText("Modify Identity Threshold...");
1253 modifyPID.addActionListener(new java.awt.event.ActionListener()
1255 public void actionPerformed(ActionEvent e)
1257 modifyPID_actionPerformed(e);
1260 modifyConservation.setText("Modify Conservation Threshold...");
1262 .addActionListener(new java.awt.event.ActionListener()
1264 public void actionPerformed(ActionEvent e)
1266 modifyConservation_actionPerformed(e);
1269 sortByTreeMenu.setText("By Tree Order");
1270 sort.setText("Sort");
1271 sort.addMenuListener(new MenuListener()
1273 public void menuSelected(MenuEvent e)
1278 public void menuDeselected(MenuEvent e)
1282 public void menuCanceled(MenuEvent e)
1286 sortByAnnotScore.setText("by Score");
1287 sort.add(sortByAnnotScore);
1288 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1291 public void menuCanceled(MenuEvent e)
1295 public void menuDeselected(MenuEvent e)
1299 public void menuSelected(MenuEvent e)
1301 buildSortByAnnotationScoresMenu();
1304 sortByAnnotScore.setVisible(false);
1306 calculateTree.setText("Calculate Tree");
1308 jMenu2.setText("Export Image");
1309 padGapsMenuitem.setText("Pad Gaps");
1310 padGapsMenuitem.setState(jalview.bin.Cache
1311 .getDefault("PAD_GAPS", false));
1312 padGapsMenuitem.addActionListener(new ActionListener()
1314 public void actionPerformed(ActionEvent e)
1316 padGapsMenuitem_actionPerformed(e);
1319 vamsasStore.setVisible(false);
1320 vamsasStore.setText("VAMSAS store");
1321 vamsasStore.addActionListener(new ActionListener()
1323 public void actionPerformed(ActionEvent e)
1325 vamsasStore_actionPerformed(e);
1328 showTranslation.setText("Translate cDNA");
1329 showTranslation.addActionListener(new ActionListener()
1331 public void actionPerformed(ActionEvent e)
1333 showTranslation_actionPerformed(e);
1336 extractScores.setText("Extract Scores...");
1337 extractScores.addActionListener(new ActionListener()
1339 public void actionPerformed(ActionEvent e)
1341 extractScores_actionPerformed(e);
1344 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1346 showProducts.setText("Get Cross References");
1348 * showProducts.addActionListener(new ActionListener() {
1350 * public void actionPerformed(ActionEvent e) {
1351 * showProducts_actionPerformed(e); } });
1353 featureSettings.setText("Feature Settings...");
1354 featureSettings.addActionListener(new ActionListener()
1356 public void actionPerformed(ActionEvent e)
1358 featureSettings_actionPerformed(e);
1361 fetchSequence.setText("Fetch Sequence(s)...");
1362 fetchSequence.addActionListener(new ActionListener()
1364 public void actionPerformed(ActionEvent e)
1366 fetchSequence_actionPerformed(e);
1370 annotationColour.setText("By Annotation...");
1371 annotationColour.addActionListener(new ActionListener()
1373 public void actionPerformed(ActionEvent e)
1375 annotationColour_actionPerformed(e);
1378 associatedData.setText("Load Features / Annotations");
1379 associatedData.addActionListener(new ActionListener()
1381 public void actionPerformed(ActionEvent e)
1383 associatedData_actionPerformed(e);
1386 autoCalculate.setText("Autocalculate Consensus");
1387 autoCalculate.setState(jalview.bin.Cache.getDefault(
1388 "AUTO_CALC_CONSENSUS", true));
1389 autoCalculate.addActionListener(new ActionListener()
1391 public void actionPerformed(ActionEvent e)
1393 autoCalculate_actionPerformed(e);
1396 addSequenceMenu.setText("Add Sequences");
1397 addFromFile.setText("From File");
1398 addFromFile.addActionListener(new ActionListener()
1400 public void actionPerformed(ActionEvent e)
1402 addFromFile_actionPerformed(e);
1405 addFromText.setText("From Textbox");
1406 addFromText.addActionListener(new ActionListener()
1408 public void actionPerformed(ActionEvent e)
1410 addFromText_actionPerformed(e);
1413 addFromURL.setText("From URL");
1414 addFromURL.addActionListener(new ActionListener()
1416 public void actionPerformed(ActionEvent e)
1418 addFromURL_actionPerformed(e);
1421 exportFeatures.setText("Export Features...");
1422 exportFeatures.addActionListener(new ActionListener()
1424 public void actionPerformed(ActionEvent e)
1426 exportFeatures_actionPerformed(e);
1429 exportAnnotations.setText("Export Annotations...");
1430 exportAnnotations.addActionListener(new ActionListener()
1432 public void actionPerformed(ActionEvent e)
1434 exportAnnotations_actionPerformed(e);
1437 statusPanel.setLayout(gridLayout1);
1438 jMenu3.setText("Show");
1439 showAllSeqs.setText("All Sequences");
1440 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1441 showAllSeqs.addActionListener(new ActionListener()
1443 public void actionPerformed(ActionEvent e)
1445 showAllSeqs_actionPerformed(e);
1448 showAllColumns.setText("All Columns");
1449 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1450 showAllColumns.addActionListener(new ActionListener()
1452 public void actionPerformed(ActionEvent e)
1454 showAllColumns_actionPerformed(e);
1457 hideMenu.setText("Hide");
1458 hideSelSequences.setText("Selected Sequences");
1459 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1460 hideSelSequences.addActionListener(new ActionListener()
1462 public void actionPerformed(ActionEvent e)
1464 hideSelSequences_actionPerformed(e);
1467 hideSelColumns.setText("Selected Columns");
1468 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1469 hideSelColumns.addActionListener(new ActionListener()
1471 public void actionPerformed(ActionEvent e)
1473 hideSelColumns_actionPerformed(e);
1476 hideAllSelection.setText("Selected Region");
1477 hideAllSelection.addActionListener(new ActionListener()
1479 public void actionPerformed(ActionEvent e)
1481 hideAllSelection_actionPerformed(e);
1484 // TODO: should be hidden if no selection exists.
1485 hideAllButSelection.setText("All but Selected Rregion (Shift+Ctrl+H)");
1486 hideAllButSelection.addActionListener(new ActionListener()
1488 public void actionPerformed(ActionEvent e)
1490 hideAllButSelection_actionPerformed(e);
1493 showAllhidden.setText("All Sequences and Columns");
1494 showAllhidden.setToolTipText("H toggles visibility of hidden or selected regions.");
1495 showAllhidden.addActionListener(new ActionListener()
1497 public void actionPerformed(ActionEvent e)
1499 showAllhidden_actionPerformed(e);
1503 hiddenMarkers.setText("Show Hidden Markers");
1504 hiddenMarkers.addActionListener(new ActionListener()
1506 public void actionPerformed(ActionEvent e)
1508 hiddenMarkers_actionPerformed(e);
1511 invertColSel.setText("Invert Column Selection");
1512 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1513 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1514 .getMenuShortcutKeyMask()
1515 | java.awt.event.KeyEvent.ALT_MASK, false));
1516 invertColSel.addActionListener(new ActionListener()
1518 public void actionPerformed(ActionEvent e)
1520 invertColSel_actionPerformed(e);
1523 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1525 public void stateChanged(ChangeEvent evt)
1527 JTabbedPane pane = (JTabbedPane) evt.getSource();
1528 int sel = pane.getSelectedIndex();
1529 tabSelectionChanged(sel);
1532 tabbedPane.addMouseListener(new MouseAdapter()
1534 public void mousePressed(MouseEvent e)
1536 tabbedPane_mousePressed(e);
1539 tabbedPane.addFocusListener(new FocusAdapter()
1541 public void focusGained(FocusEvent e)
1543 tabbedPane_focusGained(e);
1546 save.setText("Save");
1547 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1548 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1549 .getMenuShortcutKeyMask(), false));
1550 save.addActionListener(new ActionListener()
1552 public void actionPerformed(ActionEvent e)
1554 save_actionPerformed(e);
1557 reload.setEnabled(false);
1558 reload.setText("Reload");
1559 reload.addActionListener(new ActionListener()
1561 public void actionPerformed(ActionEvent e)
1563 reload_actionPerformed(e);
1566 newView.setText("New View");
1567 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1568 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1569 .getMenuShortcutKeyMask(), false));
1570 newView.addActionListener(new ActionListener()
1572 public void actionPerformed(ActionEvent e)
1574 newView_actionPerformed(e);
1577 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1578 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1579 textColour.setText("Colour Text ...");
1580 textColour.addActionListener(new ActionListener()
1582 public void actionPerformed(ActionEvent e)
1584 textColour_actionPerformed(e);
1587 formatMenu.setText("Format");
1588 selectMenu.setText("Select");
1589 idRightAlign.setText("Right Align Sequence Id");
1590 idRightAlign.addActionListener(new ActionListener()
1592 public void actionPerformed(ActionEvent e)
1594 idRightAlign_actionPerformed(e);
1597 gatherViews.setEnabled(false);
1598 gatherViews.setText("Gather Views");
1599 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1600 java.awt.event.KeyEvent.VK_G, 0, false));
1601 gatherViews.addActionListener(new ActionListener()
1603 public void actionPerformed(ActionEvent e)
1605 gatherViews_actionPerformed(e);
1608 expandViews.setEnabled(false);
1609 expandViews.setText("Expand Views");
1610 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1611 java.awt.event.KeyEvent.VK_X, 0, false));
1612 expandViews.addActionListener(new ActionListener()
1614 public void actionPerformed(ActionEvent e)
1616 expandViews_actionPerformed(e);
1619 pageSetup.setText("Page Setup ...");
1620 pageSetup.addActionListener(new ActionListener()
1622 public void actionPerformed(ActionEvent e)
1624 pageSetup_actionPerformed(e);
1627 alignmentProperties.setText("Alignment Properties...");
1628 alignmentProperties.addActionListener(new ActionListener()
1630 public void actionPerformed(ActionEvent actionEvent)
1632 alignmentProperties();
1635 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1636 autoAnnMenu.setText("Autocalculated Annotation");
1637 alignFrameMenuBar.add(fileMenu);
1638 alignFrameMenuBar.add(editMenu);
1639 alignFrameMenuBar.add(selectMenu);
1640 alignFrameMenuBar.add(viewMenu);
1641 alignFrameMenuBar.add(formatMenu);
1642 alignFrameMenuBar.add(colourMenu);
1643 alignFrameMenuBar.add(calculateMenu);
1644 alignFrameMenuBar.add(webService);
1645 fileMenu.add(fetchSequence);
1646 fileMenu.add(addSequenceMenu);
1647 fileMenu.add(reload);
1648 fileMenu.addSeparator();
1649 fileMenu.add(vamsasStore);
1651 fileMenu.add(saveAs);
1652 fileMenu.add(outputTextboxMenu);
1653 fileMenu.add(pageSetup);
1654 fileMenu.add(printMenuItem);
1655 fileMenu.addSeparator();
1656 fileMenu.add(jMenu2);
1657 fileMenu.add(exportFeatures);
1658 fileMenu.add(exportAnnotations);
1659 fileMenu.add(LoadtreeMenuItem);
1660 fileMenu.add(associatedData);
1661 fileMenu.addSeparator();
1662 fileMenu.add(closeMenuItem);
1663 editMenu.add(undoMenuItem);
1664 editMenu.add(redoMenuItem);
1667 editMenu.add(pasteMenu);
1668 editMenu.add(delete);
1669 editMenu.addSeparator();
1670 editMenu.add(remove2LeftMenuItem);
1671 editMenu.add(remove2RightMenuItem);
1672 editMenu.add(removeGappedColumnMenuItem);
1673 editMenu.add(removeAllGapsMenuItem);
1674 editMenu.add(removeRedundancyMenuItem);
1675 editMenu.addSeparator();
1676 // dont add these yet in the CVS build - they cannot be undone!
1677 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1678 // editMenu.add(justifyLeftMenuItem);
1679 // editMenu.add(justifyRightMenuItem);
1680 // editMenu.addSeparator();
1681 editMenu.add(padGapsMenuitem);
1682 viewMenu.add(newView);
1683 viewMenu.add(expandViews);
1684 viewMenu.add(gatherViews);
1685 viewMenu.addSeparator();
1686 viewMenu.add(jMenu3);
1687 viewMenu.add(hideMenu);
1688 viewMenu.addSeparator();
1689 viewMenu.add(followHighlightMenuItem);
1690 viewMenu.add(annotationPanelMenuItem);
1691 autoAnnMenu.add(applyAutoAnnotationSettings);
1692 autoAnnMenu.add(showConsensusHistogram);
1693 autoAnnMenu.add(showSequenceLogo);
1694 autoAnnMenu.addSeparator();
1695 autoAnnMenu.add(showGroupConservation);
1696 autoAnnMenu.add(showGroupConsensus);
1697 viewMenu.add(autoAnnMenu);
1698 viewMenu.addSeparator();
1699 viewMenu.add(showSeqFeatures);
1700 //viewMenu.add(showSeqFeaturesHeight);
1702 viewMenu.add(featureSettings);
1703 tooltipSettingsMenu.add(showDbRefsMenuitem);
1704 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1705 viewMenu.add(tooltipSettingsMenu);
1706 viewMenu.addSeparator();
1707 viewMenu.add(alignmentProperties);
1708 viewMenu.addSeparator();
1709 viewMenu.add(overviewMenuItem);
1710 colourMenu.add(applyToAllGroups);
1711 colourMenu.add(textColour);
1712 colourMenu.addSeparator();
1713 colourMenu.add(noColourmenuItem);
1714 colourMenu.add(clustalColour);
1715 colourMenu.add(BLOSUM62Colour);
1716 colourMenu.add(PIDColour);
1717 colourMenu.add(zappoColour);
1718 colourMenu.add(taylorColour);
1719 colourMenu.add(hydrophobicityColour);
1720 colourMenu.add(helixColour);
1721 colourMenu.add(strandColour);
1722 colourMenu.add(turnColour);
1723 colourMenu.add(buriedColour);
1724 colourMenu.add(nucleotideColour);
1725 colourMenu.add(userDefinedColour);
1726 colourMenu.addSeparator();
1727 colourMenu.add(conservationMenuItem);
1728 colourMenu.add(modifyConservation);
1729 colourMenu.add(abovePIDThreshold);
1730 colourMenu.add(modifyPID);
1731 colourMenu.add(annotationColour);
1732 calculateMenu.add(sort);
1733 calculateMenu.add(calculateTree);
1734 calculateMenu.addSeparator();
1735 calculateMenu.add(pairwiseAlignmentMenuItem);
1736 calculateMenu.add(PCAMenuItem);
1737 calculateMenu.addSeparator();
1738 calculateMenu.add(showTranslation);
1739 calculateMenu.add(showProducts);
1740 calculateMenu.add(autoCalculate);
1741 calculateMenu.addSeparator();
1742 calculateMenu.add(extractScores);
1743 webServiceNoServices = new JMenuItem("<No Services>");
1744 webService.add(webServiceNoServices);
1745 pasteMenu.add(pasteNew);
1746 pasteMenu.add(pasteThis);
1747 sort.add(sortIDMenuItem);
1748 sort.add(sortLengthMenuItem);
1749 sort.add(sortGroupMenuItem);
1750 sort.add(sortPairwiseMenuItem);
1751 sort.add(sortByTreeMenu);
1752 calculateTree.add(averageDistanceTreeMenuItem);
1753 calculateTree.add(neighbourTreeMenuItem);
1754 calculateTree.add(avDistanceTreeBlosumMenuItem);
1755 calculateTree.add(njTreeBlosumMenuItem);
1756 jMenu2.add(htmlMenuItem);
1757 jMenu2.add(epsFile);
1758 jMenu2.add(createPNG);
1759 addSequenceMenu.add(addFromFile);
1760 addSequenceMenu.add(addFromText);
1761 addSequenceMenu.add(addFromURL);
1762 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1763 statusPanel.add(statusBar, null);
1764 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1765 jMenu3.add(showAllColumns);
1766 jMenu3.add(showAllSeqs);
1767 jMenu3.add(showAllhidden);
1768 hideMenu.add(hideSelColumns);
1769 hideMenu.add(hideSelSequences);
1770 hideMenu.add(hideAllSelection);
1771 hideMenu.add(hideAllButSelection);
1773 formatMenu.add(font);
1774 formatMenu.addSeparator();
1775 formatMenu.add(wrapMenuItem);
1776 formatMenu.add(scaleAbove);
1777 formatMenu.add(scaleLeft);
1778 formatMenu.add(scaleRight);
1779 formatMenu.add(seqLimits);
1780 formatMenu.add(idRightAlign);
1781 formatMenu.add(hiddenMarkers);
1782 formatMenu.add(viewBoxesMenuItem);
1783 formatMenu.add(viewTextMenuItem);
1784 formatMenu.add(colourTextMenuItem);
1785 formatMenu.add(renderGapsMenuItem);
1786 formatMenu.add(centreColumnLabelsMenuItem);
1787 formatMenu.add(showUnconservedMenuItem);
1788 selectMenu.add(findMenuItem);
1789 selectMenu.addSeparator();
1790 selectMenu.add(selectAllSequenceMenuItem);
1791 selectMenu.add(deselectAllSequenceMenuItem);
1792 selectMenu.add(invertSequenceMenuItem);
1793 selectMenu.add(invertColSel);
1794 selectMenu.add(deleteGroups);
1795 selectMenu.add(grpsFromSelection);
1798 protected void showAllhidden_actionPerformed(ActionEvent e)
1800 // TODO Auto-generated method stub
1804 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1806 // TODO Auto-generated method stub
1810 protected void hideAllSelection_actionPerformed(ActionEvent e)
1812 // TODO Auto-generated method stub
1816 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1818 // TODO Auto-generated method stub
1822 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1824 // TODO Auto-generated method stub
1828 protected void showSequenceLogo_actionPerformed(ActionEvent e)
1830 // TODO Auto-generated method stub
1834 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1836 // TODO Auto-generated method stub
1840 protected void showGroupConsensus_actionPerformed(ActionEvent e)
1842 // TODO Auto-generated method stub
1846 protected void showGroupConservation_actionPerformed(ActionEvent e)
1848 // TODO Auto-generated method stub
1852 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1854 // TODO Auto-generated method stub
1858 protected void showSeqFeaturesHeight_actionPerformed(
1859 ActionEvent actionEvent)
1861 // TODO Auto-generated method stub
1865 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1867 // TODO Auto-generated method stub
1871 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1873 // TODO Auto-generated method stub
1877 protected void followHighlight_actionPerformed()
1879 // TODO Auto-generated method stub
1883 protected void showNpFeats_actionPerformed(ActionEvent e)
1885 // TODO Auto-generated method stub
1889 protected void showDbRefs_actionPerformed(ActionEvent e)
1891 // TODO Auto-generated method stub
1895 protected void centreColumnLabels_actionPerformed(ActionEvent e)
1899 protected void showProducts_actionPerformed(ActionEvent e)
1903 protected void buildSortByAnnotationScoresMenu()
1907 protected void extractScores_actionPerformed(ActionEvent e)
1911 protected void outputText_actionPerformed(ActionEvent e)
1915 public void addFromFile_actionPerformed(ActionEvent e)
1920 public void addFromText_actionPerformed(ActionEvent e)
1925 public void addFromURL_actionPerformed(ActionEvent e)
1930 public void exportFeatures_actionPerformed(ActionEvent e)
1935 public void exportAnnotations_actionPerformed(ActionEvent e)
1940 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1944 protected void closeMenuItem_actionPerformed(boolean b)
1948 protected void redoMenuItem_actionPerformed(ActionEvent e)
1952 protected void undoMenuItem_actionPerformed(ActionEvent e)
1956 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1960 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1964 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1968 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1972 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1976 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1980 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1984 protected void wrapMenuItem_actionPerformed(ActionEvent e)
1988 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1992 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1996 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2000 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2004 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2008 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2012 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2016 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2020 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2024 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2028 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2032 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2036 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2040 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2044 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2048 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2052 protected void clustalColour_actionPerformed(ActionEvent e)
2056 protected void zappoColour_actionPerformed(ActionEvent e)
2060 protected void taylorColour_actionPerformed(ActionEvent e)
2064 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2068 protected void helixColour_actionPerformed(ActionEvent e)
2072 protected void strandColour_actionPerformed(ActionEvent e)
2076 protected void turnColour_actionPerformed(ActionEvent e)
2080 protected void buriedColour_actionPerformed(ActionEvent e)
2084 protected void userDefinedColour_actionPerformed(ActionEvent e)
2088 protected void PIDColour_actionPerformed(ActionEvent e)
2092 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2096 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2100 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2104 protected void printMenuItem_actionPerformed(ActionEvent e)
2108 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2112 protected void findMenuItem_actionPerformed(ActionEvent e)
2116 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2120 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2124 protected void nucleotideColour_actionPerformed(ActionEvent e)
2128 protected void deleteGroups_actionPerformed(ActionEvent e)
2132 protected void copy_actionPerformed(ActionEvent e)
2136 protected void cut_actionPerformed(ActionEvent e)
2140 protected void delete_actionPerformed(ActionEvent e)
2144 protected void pasteNew_actionPerformed(ActionEvent e)
2148 protected void pasteThis_actionPerformed(ActionEvent e)
2152 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2156 public void createPNG(java.io.File f)
2160 protected void font_actionPerformed(ActionEvent e)
2164 protected void seqLimit_actionPerformed(ActionEvent e)
2168 public void seqDBRef_actionPerformed(ActionEvent e)
2173 public void createEPS(java.io.File f)
2177 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2181 protected void jpred_actionPerformed(ActionEvent e)
2185 protected void scaleAbove_actionPerformed(ActionEvent e)
2189 protected void scaleLeft_actionPerformed(ActionEvent e)
2193 protected void scaleRight_actionPerformed(ActionEvent e)
2197 protected void modifyPID_actionPerformed(ActionEvent e)
2201 protected void modifyConservation_actionPerformed(ActionEvent e)
2205 protected void saveAs_actionPerformed(ActionEvent e)
2209 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2213 public void vamsasStore_actionPerformed(ActionEvent e)
2218 public void vamsasLoad_actionPerformed(ActionEvent e)
2223 public void showTranslation_actionPerformed(ActionEvent e)
2228 public void featureSettings_actionPerformed(ActionEvent e)
2233 public void fetchSequence_actionPerformed(ActionEvent e)
2238 public void smoothFont_actionPerformed(ActionEvent e)
2243 public void annotationColour_actionPerformed(ActionEvent e)
2248 public void associatedData_actionPerformed(ActionEvent e)
2253 public void autoCalculate_actionPerformed(ActionEvent e)
2258 public void showAllSeqs_actionPerformed(ActionEvent e)
2263 public void showAllColumns_actionPerformed(ActionEvent e)
2268 public void hideSelSequences_actionPerformed(ActionEvent e)
2273 public void hideSelColumns_actionPerformed(ActionEvent e)
2278 public void hiddenMarkers_actionPerformed(ActionEvent e)
2283 public void findPdbId_actionPerformed(ActionEvent e)
2288 public void enterPdbId_actionPerformed(ActionEvent e)
2293 public void pdbFile_actionPerformed(ActionEvent e)
2298 public void invertColSel_actionPerformed(ActionEvent e)
2303 public void tabSelectionChanged(int sel)
2308 public void tabbedPane_mousePressed(MouseEvent e)
2313 public void tabbedPane_focusGained(FocusEvent e)
2318 public void save_actionPerformed(ActionEvent e)
2323 public void reload_actionPerformed(ActionEvent e)
2328 public void newView_actionPerformed(ActionEvent e)
2333 public void textColour_actionPerformed(ActionEvent e)
2338 public void idRightAlign_actionPerformed(ActionEvent e)
2343 public void expandViews_actionPerformed(ActionEvent e)
2348 public void gatherViews_actionPerformed(ActionEvent e)
2353 public void buildTreeMenu()
2358 public void pageSetup_actionPerformed(ActionEvent e)
2363 public void alignmentProperties()