2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 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;
20 import jalview.schemes.ColourSchemeProperty;
22 import java.awt.BorderLayout;
23 import java.awt.Color;
24 import java.awt.GridLayout;
25 import java.awt.Toolkit;
26 import java.awt.event.ActionEvent;
27 import java.awt.event.ActionListener;
28 import java.awt.event.FocusAdapter;
29 import java.awt.event.FocusEvent;
30 import java.awt.event.MouseAdapter;
31 import java.awt.event.MouseEvent;
33 import javax.swing.BorderFactory;
34 import javax.swing.ButtonGroup;
35 import javax.swing.JCheckBoxMenuItem;
36 import javax.swing.JInternalFrame;
37 import javax.swing.JLabel;
38 import javax.swing.JMenu;
39 import javax.swing.JMenuBar;
40 import javax.swing.JMenuItem;
41 import javax.swing.JOptionPane;
42 import javax.swing.JPanel;
43 import javax.swing.JRadioButtonMenuItem;
44 import javax.swing.JTabbedPane;
45 import javax.swing.SwingUtilities;
46 import javax.swing.event.ChangeEvent;
47 import javax.swing.event.MenuEvent;
48 import javax.swing.event.MenuListener;
50 public class GAlignFrame extends JInternalFrame
52 protected JMenuBar alignFrameMenuBar = new JMenuBar();
54 protected JMenu fileMenu = new JMenu();
56 protected JMenuItem closeMenuItem = new JMenuItem();
58 protected JMenu editMenu = new JMenu();
60 protected JMenu viewMenu = new JMenu();
62 protected JMenu colourMenu = new JMenu();
64 protected JMenu calculateMenu = new JMenu();
66 protected JMenu webService = new JMenu();
68 protected JMenuItem webServiceNoServices;
70 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
72 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
74 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
76 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
78 protected JMenuItem remove2RightMenuItem = new JMenuItem();
80 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
82 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
84 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
86 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
88 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
90 protected JMenuItem sortIDMenuItem = new JMenuItem();
92 protected JMenuItem sortLengthMenuItem = new JMenuItem();
94 protected JMenuItem sortGroupMenuItem = new JMenuItem();
96 protected JMenu sortByAnnotScore = new JMenu();
98 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
100 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
102 protected JMenuItem PCAMenuItem = new JMenuItem();
104 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
106 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
108 BorderLayout borderLayout1 = new BorderLayout();
110 public JLabel statusBar = new JLabel();
112 protected JMenuItem saveAs = new JMenuItem();
114 protected JMenu outputTextboxMenu = new JMenu();
116 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
118 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
120 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
122 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
124 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
126 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
128 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
130 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
132 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
134 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
136 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
138 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
141 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
143 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
145 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
147 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
149 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
151 JMenuItem htmlMenuItem = new JMenuItem();
153 JMenuItem overviewMenuItem = new JMenuItem();
155 protected JMenuItem undoMenuItem = new JMenuItem();
157 protected JMenuItem redoMenuItem = new JMenuItem();
159 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
161 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
163 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
165 JMenuItem printMenuItem = new JMenuItem();
167 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
169 JMenuItem findMenuItem = new JMenuItem();
171 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
173 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
175 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
177 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
179 JMenuItem deleteGroups = new JMenuItem();
181 JMenuItem delete = new JMenuItem();
183 JMenuItem copy = new JMenuItem();
185 JMenuItem cut = new JMenuItem();
187 JMenu pasteMenu = new JMenu();
189 JMenuItem pasteNew = new JMenuItem();
191 JMenuItem pasteThis = new JMenuItem();
193 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
195 JMenuItem createPNG = new JMenuItem();
197 protected JMenuItem font = new JMenuItem();
199 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
201 JMenuItem epsFile = new JMenuItem();
203 JMenuItem LoadtreeMenuItem = new JMenuItem();
205 JMenuItem loadScoresMenuItem = new JMenuItem();
207 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
209 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
211 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
213 protected JMenuItem modifyPID = new JMenuItem();
215 protected JMenuItem modifyConservation = new JMenuItem();
217 protected JMenu sortByTreeMenu = new JMenu();
219 protected JMenu sort = new JMenu();
221 protected JMenu calculateTree = new JMenu();
223 JMenu jMenu2 = new JMenu();
225 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
227 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
229 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
231 protected ButtonGroup colours = new ButtonGroup();
233 JMenuItem vamsasStore = new JMenuItem();
235 protected JMenuItem showTranslation = new JMenuItem();
237 protected JMenuItem extractScores = new JMenuItem();
239 protected JMenu showProducts = new JMenu();
241 public JMenuItem featureSettings = new JMenuItem();
243 JMenuItem fetchSequence = new JMenuItem();
245 JMenuItem annotationColour = new JMenuItem();
247 JMenuItem associatedData = new JMenuItem();
249 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
251 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
253 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
255 JMenu addSequenceMenu = new JMenu();
257 JMenuItem addFromFile = new JMenuItem();
259 JMenuItem addFromText = new JMenuItem();
261 JMenuItem addFromURL = new JMenuItem();
263 JMenuItem exportAnnotations = new JMenuItem();
265 JMenuItem exportFeatures = new JMenuItem();
267 protected JPanel statusPanel = new JPanel();
269 GridLayout gridLayout1 = new GridLayout();
271 JMenu jMenu3 = new JMenu();
273 JMenuItem showAllSeqs = new JMenuItem();
275 JMenuItem showAllColumns = new JMenuItem();
277 JMenu hideMenu = new JMenu();
279 JMenuItem hideSelSequences = new JMenuItem();
281 JMenuItem hideSelColumns = new JMenuItem();
283 JMenuItem hideAllButSelection = new JMenuItem();
285 JMenuItem hideAllSelection = new JMenuItem();
287 JMenuItem showAllhidden = new JMenuItem();
289 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
291 JMenuItem invertColSel = new JMenuItem();
293 protected JTabbedPane tabbedPane = new JTabbedPane();
295 JMenuItem save = new JMenuItem();
297 protected JMenuItem reload = new JMenuItem();
299 JMenuItem newView = new JMenuItem();
301 JMenuItem textColour = new JMenuItem();
303 JMenu formatMenu = new JMenu();
305 JMenu selectMenu = new JMenu();
307 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
309 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
311 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
313 protected JMenuItem gatherViews = new JMenuItem();
315 protected JMenuItem expandViews = new JMenuItem();
317 JMenuItem pageSetup = new JMenuItem();
319 JMenuItem alignmentProperties = new JMenuItem();
321 JMenu tooltipSettingsMenu = new JMenu();
323 private JMenuItem justifyLeftMenuItem = new JMenuItem();
325 private JMenuItem justifyRightMenuItem = new JMenuItem();
327 JMenu autoAnnMenu = new JMenu();
329 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
331 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
333 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
335 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
337 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
339 private JMenuItem grpsFromSelection = new JMenuItem();
346 setJMenuBar(alignFrameMenuBar);
348 // dynamically fill save as menu with available formats
349 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
351 JMenuItem item = new JMenuItem(
352 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
354 item.addActionListener(new java.awt.event.ActionListener()
356 public void actionPerformed(ActionEvent e)
358 outputText_actionPerformed(e);
362 outputTextboxMenu.add(item);
364 } catch (Exception e)
368 if (!new jalview.util.Platform().isAMac())
370 closeMenuItem.setMnemonic('C');
371 outputTextboxMenu.setMnemonic('T');
372 undoMenuItem.setMnemonic('Z');
373 redoMenuItem.setMnemonic('0');
374 copy.setMnemonic('C');
375 cut.setMnemonic('U');
376 pasteMenu.setMnemonic('P');
377 reload.setMnemonic('R');
380 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
382 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
383 .getUserColourSchemes().keys();
385 while (userColours.hasMoreElements())
387 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
388 userColours.nextElement().toString());
389 radioItem.setName("USER_DEFINED");
390 radioItem.addMouseListener(new MouseAdapter()
392 public void mousePressed(MouseEvent evt)
394 if (evt.isControlDown()
395 || SwingUtilities.isRightMouseButton(evt))
397 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
399 int option = JOptionPane.showInternalConfirmDialog(
400 jalview.gui.Desktop.desktop,
401 "Remove from default list?",
402 "Remove user defined colour",
403 JOptionPane.YES_NO_OPTION);
404 if (option == JOptionPane.YES_OPTION)
406 jalview.gui.UserDefinedColours
407 .removeColourFromDefaults(radioItem.getText());
408 colourMenu.remove(radioItem);
412 radioItem.addActionListener(new ActionListener()
414 public void actionPerformed(ActionEvent evt)
416 userDefinedColour_actionPerformed(evt);
423 radioItem.addActionListener(new ActionListener()
425 public void actionPerformed(ActionEvent evt)
427 userDefinedColour_actionPerformed(evt);
430 colourMenu.insert(radioItem, 15);
431 colours.add(radioItem);
434 colours.add(noColourmenuItem);
435 colours.add(clustalColour);
436 colours.add(zappoColour);
437 colours.add(taylorColour);
438 colours.add(hydrophobicityColour);
439 colours.add(helixColour);
440 colours.add(strandColour);
441 colours.add(turnColour);
442 colours.add(buriedColour);
443 colours.add(userDefinedColour);
444 colours.add(PIDColour);
445 colours.add(BLOSUM62Colour);
446 colours.add(nucleotideColour);
447 colours.add(tcoffeeColour);
449 setColourSelected(jalview.bin.Cache
450 .getDefault("DEFAULT_COLOUR", "None"));
454 public void setColourSelected(String defaultColour)
457 if (defaultColour != null)
459 int index = ColourSchemeProperty
460 .getColourIndexFromName(defaultColour);
464 case ColourSchemeProperty.CLUSTAL:
465 clustalColour.setSelected(true);
469 case ColourSchemeProperty.BLOSUM:
470 BLOSUM62Colour.setSelected(true);
474 case ColourSchemeProperty.PID:
475 PIDColour.setSelected(true);
479 case ColourSchemeProperty.ZAPPO:
480 zappoColour.setSelected(true);
484 case ColourSchemeProperty.TAYLOR:
485 taylorColour.setSelected(true);
488 case ColourSchemeProperty.HYDROPHOBIC:
489 hydrophobicityColour.setSelected(true);
493 case ColourSchemeProperty.HELIX:
494 helixColour.setSelected(true);
498 case ColourSchemeProperty.STRAND:
499 strandColour.setSelected(true);
503 case ColourSchemeProperty.TURN:
504 turnColour.setSelected(true);
508 case ColourSchemeProperty.BURIED:
509 buriedColour.setSelected(true);
513 case ColourSchemeProperty.NUCLEOTIDE:
514 nucleotideColour.setSelected(true);
518 case ColourSchemeProperty.TCOFFEE:
519 tcoffeeColour.setSelected(true);
522 case ColourSchemeProperty.USER_DEFINED:
523 userDefinedColour.setSelected(true);
526 case ColourSchemeProperty.NONE:
528 noColourmenuItem.setSelected(true);
536 private void jbInit() throws Exception
538 fileMenu.setText("File");
539 saveAs.setText("Save As...");
540 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
541 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
542 .getMenuShortcutKeyMask()
543 | java.awt.event.KeyEvent.SHIFT_MASK, false));
544 saveAs.addActionListener(new ActionListener()
546 public void actionPerformed(ActionEvent e)
548 saveAs_actionPerformed(e);
551 closeMenuItem.setText("Close");
552 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
553 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
554 .getMenuShortcutKeyMask(), false));
555 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
557 public void actionPerformed(ActionEvent e)
559 closeMenuItem_actionPerformed(false);
562 editMenu.setText("Edit");
563 viewMenu.setText("View");
564 colourMenu.setText("Colour");
565 calculateMenu.setText("Calculate");
566 webService.setText("Web Service");
567 selectAllSequenceMenuItem.setText("Select All");
568 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
569 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
570 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
571 selectAllSequenceMenuItem
572 .addActionListener(new java.awt.event.ActionListener()
574 public void actionPerformed(ActionEvent e)
576 selectAllSequenceMenuItem_actionPerformed(e);
579 deselectAllSequenceMenuItem.setText("Deselect All");
580 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
581 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
582 deselectAllSequenceMenuItem
583 .addActionListener(new java.awt.event.ActionListener()
585 public void actionPerformed(ActionEvent e)
587 deselectAllSequenceMenuItem_actionPerformed(e);
590 invertSequenceMenuItem.setText("Invert Sequence Selection");
591 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
592 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
593 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
594 invertSequenceMenuItem
595 .addActionListener(new java.awt.event.ActionListener()
597 public void actionPerformed(ActionEvent e)
599 invertSequenceMenuItem_actionPerformed(e);
602 grpsFromSelection.setText("Make Groups for selection");
603 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
605 public void actionPerformed(ActionEvent e)
607 makeGrpsFromSelection_actionPerformed(e);
611 remove2LeftMenuItem.setText("Remove Left");
612 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
613 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
614 .getMenuShortcutKeyMask(), false));
616 .addActionListener(new java.awt.event.ActionListener()
618 public void actionPerformed(ActionEvent e)
620 remove2LeftMenuItem_actionPerformed(e);
623 remove2RightMenuItem.setText("Remove Right");
624 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
625 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
626 .getMenuShortcutKeyMask(), false));
628 .addActionListener(new java.awt.event.ActionListener()
630 public void actionPerformed(ActionEvent e)
632 remove2RightMenuItem_actionPerformed(e);
635 removeGappedColumnMenuItem.setText("Remove Empty Columns");
636 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
637 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
638 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
639 removeGappedColumnMenuItem
640 .addActionListener(new java.awt.event.ActionListener()
642 public void actionPerformed(ActionEvent e)
644 removeGappedColumnMenuItem_actionPerformed(e);
647 removeAllGapsMenuItem.setText("Remove All Gaps");
648 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
649 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
650 .getDefaultToolkit().getMenuShortcutKeyMask()
651 | java.awt.event.KeyEvent.SHIFT_MASK, false));
652 removeAllGapsMenuItem
653 .addActionListener(new java.awt.event.ActionListener()
655 public void actionPerformed(ActionEvent e)
657 removeAllGapsMenuItem_actionPerformed(e);
660 justifyLeftMenuItem.setText("Left Justify Alignment");
662 .addActionListener(new java.awt.event.ActionListener()
664 public void actionPerformed(ActionEvent e)
666 justifyLeftMenuItem_actionPerformed(e);
669 justifyRightMenuItem.setText("Right Justify Alignment");
671 .addActionListener(new java.awt.event.ActionListener()
673 public void actionPerformed(ActionEvent e)
675 justifyRightMenuItem_actionPerformed(e);
678 viewBoxesMenuItem.setText("Boxes");
679 viewBoxesMenuItem.setState(true);
680 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
682 public void actionPerformed(ActionEvent e)
684 viewBoxesMenuItem_actionPerformed(e);
687 viewTextMenuItem.setText("Text");
688 viewTextMenuItem.setState(true);
689 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
691 public void actionPerformed(ActionEvent e)
693 viewTextMenuItem_actionPerformed(e);
696 showNonconservedMenuItem.setText("Show nonconserved");
697 showNonconservedMenuItem.setState(false);
698 showNonconservedMenuItem
699 .addActionListener(new java.awt.event.ActionListener()
701 public void actionPerformed(ActionEvent e)
703 showUnconservedMenuItem_actionPerformed(e);
706 sortPairwiseMenuItem.setText("by Pairwise Identity");
708 .addActionListener(new java.awt.event.ActionListener()
710 public void actionPerformed(ActionEvent e)
712 sortPairwiseMenuItem_actionPerformed(e);
715 sortIDMenuItem.setText("by ID");
716 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
718 public void actionPerformed(ActionEvent e)
720 sortIDMenuItem_actionPerformed(e);
723 sortLengthMenuItem.setText("By Length");
725 .addActionListener(new java.awt.event.ActionListener()
727 public void actionPerformed(ActionEvent e)
729 sortLengthMenuItem_actionPerformed(e);
732 sortGroupMenuItem.setText("by Group");
733 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
735 public void actionPerformed(ActionEvent e)
737 sortGroupMenuItem_actionPerformed(e);
740 removeRedundancyMenuItem.setText("Remove Redundancy...");
741 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
742 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
743 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
744 removeRedundancyMenuItem
745 .addActionListener(new java.awt.event.ActionListener()
747 public void actionPerformed(ActionEvent e)
749 removeRedundancyMenuItem_actionPerformed(e);
752 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
753 pairwiseAlignmentMenuItem
754 .addActionListener(new java.awt.event.ActionListener()
756 public void actionPerformed(ActionEvent e)
758 pairwiseAlignmentMenuItem_actionPerformed(e);
761 PCAMenuItem.setText("Principal Component Analysis");
762 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
764 public void actionPerformed(ActionEvent e)
766 PCAMenuItem_actionPerformed(e);
769 averageDistanceTreeMenuItem
770 .setText("Average Distance Using % Identity");
771 averageDistanceTreeMenuItem
772 .addActionListener(new java.awt.event.ActionListener()
774 public void actionPerformed(ActionEvent e)
776 averageDistanceTreeMenuItem_actionPerformed(e);
779 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
780 neighbourTreeMenuItem
781 .addActionListener(new java.awt.event.ActionListener()
783 public void actionPerformed(ActionEvent e)
785 neighbourTreeMenuItem_actionPerformed(e);
788 this.getContentPane().setLayout(borderLayout1);
789 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
790 statusBar.setBackground(Color.white);
791 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
792 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
793 statusBar.setText("Status bar");
794 outputTextboxMenu.setText("Output to Textbox");
795 clustalColour.setText("Clustalx");
797 clustalColour.addActionListener(new java.awt.event.ActionListener()
799 public void actionPerformed(ActionEvent e)
801 clustalColour_actionPerformed(e);
804 zappoColour.setText("Zappo");
805 zappoColour.addActionListener(new java.awt.event.ActionListener()
807 public void actionPerformed(ActionEvent e)
809 zappoColour_actionPerformed(e);
812 taylorColour.setText("Taylor");
813 taylorColour.addActionListener(new java.awt.event.ActionListener()
815 public void actionPerformed(ActionEvent e)
817 taylorColour_actionPerformed(e);
820 hydrophobicityColour.setText("Hydrophobicity");
822 .addActionListener(new java.awt.event.ActionListener()
824 public void actionPerformed(ActionEvent e)
826 hydrophobicityColour_actionPerformed(e);
829 helixColour.setText("Helix Propensity");
830 helixColour.addActionListener(new java.awt.event.ActionListener()
832 public void actionPerformed(ActionEvent e)
834 helixColour_actionPerformed(e);
837 strandColour.setText("Strand Propensity");
838 strandColour.addActionListener(new java.awt.event.ActionListener()
840 public void actionPerformed(ActionEvent e)
842 strandColour_actionPerformed(e);
845 turnColour.setText("Turn Propensity");
846 turnColour.addActionListener(new java.awt.event.ActionListener()
848 public void actionPerformed(ActionEvent e)
850 turnColour_actionPerformed(e);
853 buriedColour.setText("Buried Index");
854 buriedColour.addActionListener(new java.awt.event.ActionListener()
856 public void actionPerformed(ActionEvent e)
858 buriedColour_actionPerformed(e);
861 userDefinedColour.setText("User Defined...");
862 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
864 public void actionPerformed(ActionEvent e)
866 userDefinedColour_actionPerformed(e);
869 PIDColour.setText("Percentage Identity");
870 PIDColour.addActionListener(new java.awt.event.ActionListener()
872 public void actionPerformed(ActionEvent e)
874 PIDColour_actionPerformed(e);
877 BLOSUM62Colour.setText("BLOSUM62 Score");
878 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
880 public void actionPerformed(ActionEvent e)
882 BLOSUM62Colour_actionPerformed(e);
885 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
886 avDistanceTreeBlosumMenuItem
887 .addActionListener(new java.awt.event.ActionListener()
889 public void actionPerformed(ActionEvent e)
891 avTreeBlosumMenuItem_actionPerformed(e);
894 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
896 .addActionListener(new java.awt.event.ActionListener()
898 public void actionPerformed(ActionEvent e)
900 njTreeBlosumMenuItem_actionPerformed(e);
903 annotationPanelMenuItem.setActionCommand("");
904 annotationPanelMenuItem.setText("Show Annotations");
905 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
906 "SHOW_ANNOTATIONS", true));
907 annotationPanelMenuItem
908 .addActionListener(new java.awt.event.ActionListener()
910 public void actionPerformed(ActionEvent e)
912 annotationPanelMenuItem_actionPerformed(e);
915 colourTextMenuItem.setText("Colour Text");
917 .addActionListener(new java.awt.event.ActionListener()
919 public void actionPerformed(ActionEvent e)
921 colourTextMenuItem_actionPerformed(e);
924 htmlMenuItem.setText("HTML");
925 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
927 public void actionPerformed(ActionEvent e)
929 htmlMenuItem_actionPerformed(e);
932 overviewMenuItem.setText("Overview Window");
933 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
935 public void actionPerformed(ActionEvent e)
937 overviewMenuItem_actionPerformed(e);
940 undoMenuItem.setEnabled(false);
941 undoMenuItem.setText("Undo");
942 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
943 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
944 .getMenuShortcutKeyMask(), false));
945 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
947 public void actionPerformed(ActionEvent e)
949 undoMenuItem_actionPerformed(e);
952 redoMenuItem.setEnabled(false);
953 redoMenuItem.setText("Redo");
954 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
955 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
956 .getMenuShortcutKeyMask(), false));
957 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
959 public void actionPerformed(ActionEvent e)
961 redoMenuItem_actionPerformed(e);
964 conservationMenuItem.setText("By Conservation");
966 .addActionListener(new java.awt.event.ActionListener()
968 public void actionPerformed(ActionEvent e)
970 conservationMenuItem_actionPerformed(e);
973 noColourmenuItem.setText("None");
974 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
976 public void actionPerformed(ActionEvent e)
978 noColourmenuItem_actionPerformed(e);
981 wrapMenuItem.setText("Wrap");
982 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
984 public void actionPerformed(ActionEvent e)
986 wrapMenuItem_actionPerformed(e);
989 printMenuItem.setText("Print ...");
990 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
991 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
992 .getMenuShortcutKeyMask(), false));
993 printMenuItem.addActionListener(new java.awt.event.ActionListener()
995 public void actionPerformed(ActionEvent e)
997 printMenuItem_actionPerformed(e);
1000 renderGapsMenuItem.setText("Show Gaps");
1001 renderGapsMenuItem.setState(true);
1003 .addActionListener(new java.awt.event.ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 renderGapsMenuItem_actionPerformed(e);
1010 findMenuItem.setText("Find...");
1011 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1012 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1013 .getMenuShortcutKeyMask(), false));
1014 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1016 public void actionPerformed(ActionEvent e)
1018 findMenuItem_actionPerformed(e);
1021 abovePIDThreshold.setText("Above Identity Threshold");
1022 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1024 public void actionPerformed(ActionEvent e)
1026 abovePIDThreshold_actionPerformed(e);
1029 showSeqFeatures.setText("Show Sequence Features");
1030 showSeqFeatures.addActionListener(new ActionListener()
1032 public void actionPerformed(ActionEvent actionEvent)
1034 showSeqFeatures_actionPerformed(actionEvent);
1038 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1039 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1040 * void actionPerformed(ActionEvent actionEvent) {
1041 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1043 showDbRefsMenuitem.setText("Show Database Refs");
1044 showDbRefsMenuitem.addActionListener(new ActionListener()
1047 public void actionPerformed(ActionEvent e)
1049 showDbRefs_actionPerformed(e);
1053 showNpFeatsMenuitem.setText("Show Non-Positional Features");
1054 showNpFeatsMenuitem.addActionListener(new ActionListener()
1057 public void actionPerformed(ActionEvent e)
1059 showNpFeats_actionPerformed(e);
1063 showGroupConservation.setText("Group Conservation");
1064 showGroupConservation.addActionListener(new ActionListener()
1067 public void actionPerformed(ActionEvent e)
1069 showGroupConservation_actionPerformed(e);
1074 showGroupConsensus.setText("Group Consensus");
1075 showGroupConsensus.addActionListener(new ActionListener()
1078 public void actionPerformed(ActionEvent e)
1080 showGroupConsensus_actionPerformed(e);
1084 showConsensusHistogram.setText("Show Consensus Histogram");
1085 showConsensusHistogram.addActionListener(new ActionListener()
1088 public void actionPerformed(ActionEvent e)
1090 showConsensusHistogram_actionPerformed(e);
1094 showSequenceLogo.setText("Show Consensus Logo");
1095 showSequenceLogo.addActionListener(new ActionListener()
1098 public void actionPerformed(ActionEvent e)
1100 showSequenceLogo_actionPerformed(e);
1104 applyAutoAnnotationSettings.setText("Apply to all groups");
1105 applyAutoAnnotationSettings.setState(false);
1106 applyAutoAnnotationSettings.setVisible(true);
1107 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1110 public void actionPerformed(ActionEvent e)
1112 applyAutoAnnotationSettings_actionPerformed(e);
1117 nucleotideColour.setText("Nucleotide");
1118 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1120 public void actionPerformed(ActionEvent e)
1122 nucleotideColour_actionPerformed(e);
1126 tcoffeeColour.setText("T-Coffee scores");
1127 tcoffeeColour.setEnabled(false);
1128 tcoffeeColour.addActionListener( new ActionListener() {
1131 public void actionPerformed(ActionEvent e) {
1132 tcoffeeColorScheme_actionPerformed(e);
1137 deleteGroups.setText("Undefine groups");
1138 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1139 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1140 .getMenuShortcutKeyMask(), false));
1141 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1143 public void actionPerformed(ActionEvent e)
1145 deleteGroups_actionPerformed(e);
1148 copy.setText("Copy");
1149 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1150 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1151 .getMenuShortcutKeyMask(), false));
1153 copy.addActionListener(new java.awt.event.ActionListener()
1155 public void actionPerformed(ActionEvent e)
1157 copy_actionPerformed(e);
1161 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1162 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1163 .getMenuShortcutKeyMask(), false));
1164 cut.addActionListener(new java.awt.event.ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 cut_actionPerformed(e);
1171 delete.setText("Delete");
1172 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1173 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1174 delete.addActionListener(new java.awt.event.ActionListener()
1176 public void actionPerformed(ActionEvent e)
1178 delete_actionPerformed(e);
1181 pasteMenu.setText("Paste");
1182 pasteNew.setText("To New Alignment");
1183 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1184 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1185 .getMenuShortcutKeyMask()
1186 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1187 pasteNew.addActionListener(new java.awt.event.ActionListener()
1189 public void actionPerformed(ActionEvent e)
1191 pasteNew_actionPerformed(e);
1194 pasteThis.setText("Add To This Alignment");
1195 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1196 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1197 .getMenuShortcutKeyMask(), false));
1198 pasteThis.addActionListener(new java.awt.event.ActionListener()
1200 public void actionPerformed(ActionEvent e)
1202 pasteThis_actionPerformed(e);
1205 applyToAllGroups.setText("Apply Colour To All Groups");
1206 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1208 public void actionPerformed(ActionEvent e)
1210 applyToAllGroups_actionPerformed(e);
1213 createPNG.addActionListener(new java.awt.event.ActionListener()
1215 public void actionPerformed(ActionEvent e)
1220 createPNG.setActionCommand("Save As PNG Image");
1221 createPNG.setText("PNG");
1222 font.setText("Font...");
1223 font.addActionListener(new java.awt.event.ActionListener()
1225 public void actionPerformed(ActionEvent e)
1227 font_actionPerformed(e);
1231 seqLimits.setText("Show Sequence Limits");
1232 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1233 seqLimits.addActionListener(new java.awt.event.ActionListener()
1235 public void actionPerformed(ActionEvent e)
1237 seqLimit_actionPerformed(e);
1240 epsFile.setText("EPS");
1241 epsFile.addActionListener(new java.awt.event.ActionListener()
1243 public void actionPerformed(ActionEvent e)
1248 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1249 LoadtreeMenuItem.setText("Load Associated Tree");
1250 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1252 public void actionPerformed(ActionEvent e)
1254 LoadtreeMenuItem_actionPerformed(e);
1258 loadScoresMenuItem.setActionCommand("Load T-Coffee scores");
1259 loadScoresMenuItem.setText("Load T-Coffee scores");
1260 loadScoresMenuItem.addActionListener(new ActionListener() {
1263 public void actionPerformed(ActionEvent e) {
1264 loadScores_actionPerformed(e);
1268 scaleAbove.setVisible(false);
1269 scaleAbove.setText("Scale Above");
1270 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1272 public void actionPerformed(ActionEvent e)
1274 scaleAbove_actionPerformed(e);
1277 scaleLeft.setVisible(false);
1278 scaleLeft.setSelected(true);
1279 scaleLeft.setText("Scale Left");
1280 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1282 public void actionPerformed(ActionEvent e)
1284 scaleLeft_actionPerformed(e);
1287 scaleRight.setVisible(false);
1288 scaleRight.setSelected(true);
1289 scaleRight.setText("Scale Right");
1290 scaleRight.addActionListener(new java.awt.event.ActionListener()
1292 public void actionPerformed(ActionEvent e)
1294 scaleRight_actionPerformed(e);
1297 centreColumnLabelsMenuItem.setVisible(true);
1298 centreColumnLabelsMenuItem.setState(false);
1299 centreColumnLabelsMenuItem.setText("Centre Column Labels");
1300 centreColumnLabelsMenuItem
1301 .addActionListener(new java.awt.event.ActionListener()
1303 public void actionPerformed(ActionEvent e)
1305 centreColumnLabels_actionPerformed(e);
1308 followHighlightMenuItem.setVisible(true);
1309 followHighlightMenuItem.setState(true);
1310 followHighlightMenuItem.setText("Automatic Scrolling");
1311 followHighlightMenuItem.addActionListener(new ActionListener()
1314 public void actionPerformed(ActionEvent e)
1316 followHighlight_actionPerformed();
1321 modifyPID.setText("Modify Identity Threshold...");
1322 modifyPID.addActionListener(new java.awt.event.ActionListener()
1324 public void actionPerformed(ActionEvent e)
1326 modifyPID_actionPerformed(e);
1329 modifyConservation.setText("Modify Conservation Threshold...");
1331 .addActionListener(new java.awt.event.ActionListener()
1333 public void actionPerformed(ActionEvent e)
1335 modifyConservation_actionPerformed(e);
1338 sortByTreeMenu.setText("By Tree Order");
1339 sort.setText("Sort");
1340 sort.addMenuListener(new MenuListener()
1342 public void menuSelected(MenuEvent e)
1347 public void menuDeselected(MenuEvent e)
1351 public void menuCanceled(MenuEvent e)
1355 sortByAnnotScore.setText("by Score");
1356 sort.add(sortByAnnotScore);
1357 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1360 public void menuCanceled(MenuEvent e)
1364 public void menuDeselected(MenuEvent e)
1368 public void menuSelected(MenuEvent e)
1370 buildSortByAnnotationScoresMenu();
1373 sortByAnnotScore.setVisible(false);
1375 calculateTree.setText("Calculate Tree");
1377 jMenu2.setText("Export Image");
1378 padGapsMenuitem.setText("Pad Gaps");
1379 padGapsMenuitem.setState(jalview.bin.Cache
1380 .getDefault("PAD_GAPS", false));
1381 padGapsMenuitem.addActionListener(new ActionListener()
1383 public void actionPerformed(ActionEvent e)
1385 padGapsMenuitem_actionPerformed(e);
1388 vamsasStore.setVisible(false);
1389 vamsasStore.setText("VAMSAS store");
1390 vamsasStore.addActionListener(new ActionListener()
1392 public void actionPerformed(ActionEvent e)
1394 vamsasStore_actionPerformed(e);
1397 showTranslation.setText("Translate cDNA");
1398 showTranslation.addActionListener(new ActionListener()
1400 public void actionPerformed(ActionEvent e)
1402 showTranslation_actionPerformed(e);
1405 extractScores.setText("Extract Scores...");
1406 extractScores.addActionListener(new ActionListener()
1408 public void actionPerformed(ActionEvent e)
1410 extractScores_actionPerformed(e);
1413 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1415 showProducts.setText("Get Cross References");
1417 * showProducts.addActionListener(new ActionListener() {
1419 * public void actionPerformed(ActionEvent e) {
1420 * showProducts_actionPerformed(e); } });
1422 featureSettings.setText("Feature Settings...");
1423 featureSettings.addActionListener(new ActionListener()
1425 public void actionPerformed(ActionEvent e)
1427 featureSettings_actionPerformed(e);
1430 fetchSequence.setText("Fetch Sequence(s)...");
1431 fetchSequence.addActionListener(new ActionListener()
1433 public void actionPerformed(ActionEvent e)
1435 fetchSequence_actionPerformed(e);
1439 annotationColour.setText("By Annotation...");
1440 annotationColour.addActionListener(new ActionListener()
1442 public void actionPerformed(ActionEvent e)
1444 annotationColour_actionPerformed(e);
1447 associatedData.setText("Load Features / Annotations");
1448 associatedData.addActionListener(new ActionListener()
1450 public void actionPerformed(ActionEvent e)
1452 associatedData_actionPerformed(e);
1455 autoCalculate.setText("Autocalculate Consensus");
1456 autoCalculate.setState(jalview.bin.Cache.getDefault(
1457 "AUTO_CALC_CONSENSUS", true));
1458 autoCalculate.addActionListener(new ActionListener()
1460 public void actionPerformed(ActionEvent e)
1462 autoCalculate_actionPerformed(e);
1465 sortByTree.setText("Sort Alignment With New Tree");
1466 sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1467 sortByTree.setState(jalview.bin.Cache.getDefault(
1468 "SORT_BY_TREE", false));
1469 sortByTree.addActionListener(new ActionListener()
1471 public void actionPerformed(ActionEvent e)
1473 sortByTreeOption_actionPerformed(e);
1477 listenToViewSelections.setText("Listen for selections");
1478 listenToViewSelections.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1479 listenToViewSelections.setState(false);
1480 listenToViewSelections.addActionListener(new ActionListener()
1482 public void actionPerformed(ActionEvent e)
1484 listenToViewSelections_actionPerformed(e);
1488 addSequenceMenu.setText("Add Sequences");
1489 addFromFile.setText("From File");
1490 addFromFile.addActionListener(new ActionListener()
1492 public void actionPerformed(ActionEvent e)
1494 addFromFile_actionPerformed(e);
1497 addFromText.setText("From Textbox");
1498 addFromText.addActionListener(new ActionListener()
1500 public void actionPerformed(ActionEvent e)
1502 addFromText_actionPerformed(e);
1505 addFromURL.setText("From URL");
1506 addFromURL.addActionListener(new ActionListener()
1508 public void actionPerformed(ActionEvent e)
1510 addFromURL_actionPerformed(e);
1513 exportFeatures.setText("Export Features...");
1514 exportFeatures.addActionListener(new ActionListener()
1516 public void actionPerformed(ActionEvent e)
1518 exportFeatures_actionPerformed(e);
1521 exportAnnotations.setText("Export Annotations...");
1522 exportAnnotations.addActionListener(new ActionListener()
1524 public void actionPerformed(ActionEvent e)
1526 exportAnnotations_actionPerformed(e);
1529 statusPanel.setLayout(gridLayout1);
1530 jMenu3.setText("Show");
1531 showAllSeqs.setText("All Sequences");
1532 showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1533 showAllSeqs.addActionListener(new ActionListener()
1535 public void actionPerformed(ActionEvent e)
1537 showAllSeqs_actionPerformed(e);
1540 showAllColumns.setText("All Columns");
1541 showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1542 showAllColumns.addActionListener(new ActionListener()
1544 public void actionPerformed(ActionEvent e)
1546 showAllColumns_actionPerformed(e);
1549 hideMenu.setText("Hide");
1550 hideSelSequences.setText("Selected Sequences");
1551 hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1552 hideSelSequences.addActionListener(new ActionListener()
1554 public void actionPerformed(ActionEvent e)
1556 hideSelSequences_actionPerformed(e);
1559 hideSelColumns.setText("Selected Columns");
1560 hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1561 hideSelColumns.addActionListener(new ActionListener()
1563 public void actionPerformed(ActionEvent e)
1565 hideSelColumns_actionPerformed(e);
1568 hideAllSelection.setText("Selected Region");
1569 hideAllSelection.addActionListener(new ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 hideAllSelection_actionPerformed(e);
1576 // TODO: should be hidden if no selection exists.
1577 hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1578 hideAllButSelection.addActionListener(new ActionListener()
1580 public void actionPerformed(ActionEvent e)
1582 hideAllButSelection_actionPerformed(e);
1585 showAllhidden.setText("All Sequences and Columns");
1587 .setToolTipText("H toggles visibility of hidden or selected regions.");
1588 showAllhidden.addActionListener(new ActionListener()
1590 public void actionPerformed(ActionEvent e)
1592 showAllhidden_actionPerformed(e);
1596 hiddenMarkers.setText("Show Hidden Markers");
1597 hiddenMarkers.addActionListener(new ActionListener()
1599 public void actionPerformed(ActionEvent e)
1601 hiddenMarkers_actionPerformed(e);
1604 invertColSel.setText("Invert Column Selection");
1605 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1606 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1607 .getMenuShortcutKeyMask()
1608 | java.awt.event.KeyEvent.ALT_MASK, false));
1609 invertColSel.addActionListener(new ActionListener()
1611 public void actionPerformed(ActionEvent e)
1613 invertColSel_actionPerformed(e);
1616 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1618 public void stateChanged(ChangeEvent evt)
1620 JTabbedPane pane = (JTabbedPane) evt.getSource();
1621 int sel = pane.getSelectedIndex();
1622 tabSelectionChanged(sel);
1625 tabbedPane.addMouseListener(new MouseAdapter()
1627 public void mousePressed(MouseEvent e)
1629 tabbedPane_mousePressed(e);
1632 tabbedPane.addFocusListener(new FocusAdapter()
1634 public void focusGained(FocusEvent e)
1636 tabbedPane_focusGained(e);
1639 save.setText("Save");
1640 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1641 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1642 .getMenuShortcutKeyMask(), false));
1643 save.addActionListener(new ActionListener()
1645 public void actionPerformed(ActionEvent e)
1647 save_actionPerformed(e);
1650 reload.setEnabled(false);
1651 reload.setText("Reload");
1652 reload.addActionListener(new ActionListener()
1654 public void actionPerformed(ActionEvent e)
1656 reload_actionPerformed(e);
1659 newView.setText("New View");
1660 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1661 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1662 .getMenuShortcutKeyMask(), false));
1663 newView.addActionListener(new ActionListener()
1665 public void actionPerformed(ActionEvent e)
1667 newView_actionPerformed(e);
1670 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1671 + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1672 textColour.setText("Colour Text ...");
1673 textColour.addActionListener(new ActionListener()
1675 public void actionPerformed(ActionEvent e)
1677 textColour_actionPerformed(e);
1680 formatMenu.setText("Format");
1681 selectMenu.setText("Select");
1682 idRightAlign.setText("Right Align Sequence Id");
1683 idRightAlign.addActionListener(new ActionListener()
1685 public void actionPerformed(ActionEvent e)
1687 idRightAlign_actionPerformed(e);
1690 gatherViews.setEnabled(false);
1691 gatherViews.setText("Gather Views");
1692 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1693 java.awt.event.KeyEvent.VK_G, 0, false));
1694 gatherViews.addActionListener(new ActionListener()
1696 public void actionPerformed(ActionEvent e)
1698 gatherViews_actionPerformed(e);
1701 expandViews.setEnabled(false);
1702 expandViews.setText("Expand Views");
1703 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1704 java.awt.event.KeyEvent.VK_X, 0, false));
1705 expandViews.addActionListener(new ActionListener()
1707 public void actionPerformed(ActionEvent e)
1709 expandViews_actionPerformed(e);
1712 pageSetup.setText("Page Setup ...");
1713 pageSetup.addActionListener(new ActionListener()
1715 public void actionPerformed(ActionEvent e)
1717 pageSetup_actionPerformed(e);
1720 alignmentProperties.setText("Alignment Properties...");
1721 alignmentProperties.addActionListener(new ActionListener()
1723 public void actionPerformed(ActionEvent actionEvent)
1725 alignmentProperties();
1728 tooltipSettingsMenu.setText("Sequence ID Tooltip");
1729 autoAnnMenu.setText("Autocalculated Annotation");
1730 alignFrameMenuBar.add(fileMenu);
1731 alignFrameMenuBar.add(editMenu);
1732 alignFrameMenuBar.add(selectMenu);
1733 alignFrameMenuBar.add(viewMenu);
1734 alignFrameMenuBar.add(formatMenu);
1735 alignFrameMenuBar.add(colourMenu);
1736 alignFrameMenuBar.add(calculateMenu);
1737 alignFrameMenuBar.add(webService);
1738 fileMenu.add(fetchSequence);
1739 fileMenu.add(addSequenceMenu);
1740 fileMenu.add(reload);
1741 fileMenu.addSeparator();
1742 fileMenu.add(vamsasStore);
1744 fileMenu.add(saveAs);
1745 fileMenu.add(outputTextboxMenu);
1746 fileMenu.add(pageSetup);
1747 fileMenu.add(printMenuItem);
1748 fileMenu.addSeparator();
1749 fileMenu.add(jMenu2);
1750 fileMenu.add(exportFeatures);
1751 fileMenu.add(exportAnnotations);
1752 fileMenu.add(LoadtreeMenuItem);
1753 fileMenu.add(associatedData);
1754 fileMenu.add(loadScoresMenuItem);
1755 fileMenu.addSeparator();
1756 fileMenu.add(closeMenuItem);
1757 editMenu.add(undoMenuItem);
1758 editMenu.add(redoMenuItem);
1761 editMenu.add(pasteMenu);
1762 editMenu.add(delete);
1763 editMenu.addSeparator();
1764 editMenu.add(remove2LeftMenuItem);
1765 editMenu.add(remove2RightMenuItem);
1766 editMenu.add(removeGappedColumnMenuItem);
1767 editMenu.add(removeAllGapsMenuItem);
1768 editMenu.add(removeRedundancyMenuItem);
1769 editMenu.addSeparator();
1770 // dont add these yet in the CVS build - they cannot be undone!
1771 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1772 // editMenu.add(justifyLeftMenuItem);
1773 // editMenu.add(justifyRightMenuItem);
1774 // editMenu.addSeparator();
1775 editMenu.add(padGapsMenuitem);
1776 viewMenu.add(newView);
1777 viewMenu.add(expandViews);
1778 viewMenu.add(gatherViews);
1779 viewMenu.addSeparator();
1780 viewMenu.add(jMenu3);
1781 viewMenu.add(hideMenu);
1782 viewMenu.addSeparator();
1783 viewMenu.add(followHighlightMenuItem);
1784 viewMenu.add(annotationPanelMenuItem);
1785 autoAnnMenu.add(applyAutoAnnotationSettings);
1786 autoAnnMenu.add(showConsensusHistogram);
1787 autoAnnMenu.add(showSequenceLogo);
1788 autoAnnMenu.addSeparator();
1789 autoAnnMenu.add(showGroupConservation);
1790 autoAnnMenu.add(showGroupConsensus);
1791 viewMenu.add(autoAnnMenu);
1792 viewMenu.addSeparator();
1793 viewMenu.add(showSeqFeatures);
1794 // viewMenu.add(showSeqFeaturesHeight);
1796 viewMenu.add(featureSettings);
1797 tooltipSettingsMenu.add(showDbRefsMenuitem);
1798 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1799 viewMenu.add(tooltipSettingsMenu);
1800 viewMenu.addSeparator();
1801 viewMenu.add(alignmentProperties);
1802 viewMenu.addSeparator();
1803 viewMenu.add(overviewMenuItem);
1804 colourMenu.add(applyToAllGroups);
1805 colourMenu.add(textColour);
1806 colourMenu.addSeparator();
1807 colourMenu.add(noColourmenuItem);
1808 colourMenu.add(clustalColour);
1809 colourMenu.add(BLOSUM62Colour);
1810 colourMenu.add(PIDColour);
1811 colourMenu.add(zappoColour);
1812 colourMenu.add(taylorColour);
1813 colourMenu.add(hydrophobicityColour);
1814 colourMenu.add(helixColour);
1815 colourMenu.add(strandColour);
1816 colourMenu.add(turnColour);
1817 colourMenu.add(buriedColour);
1818 colourMenu.add(nucleotideColour);
1819 colourMenu.add(tcoffeeColour);
1820 colourMenu.add(userDefinedColour);
1821 colourMenu.addSeparator();
1822 colourMenu.add(conservationMenuItem);
1823 colourMenu.add(modifyConservation);
1824 colourMenu.add(abovePIDThreshold);
1825 colourMenu.add(modifyPID);
1826 colourMenu.add(annotationColour);
1827 calculateMenu.add(sort);
1828 calculateMenu.add(calculateTree);
1829 calculateMenu.addSeparator();
1830 calculateMenu.add(pairwiseAlignmentMenuItem);
1831 calculateMenu.add(PCAMenuItem);
1832 calculateMenu.addSeparator();
1833 calculateMenu.add(showTranslation);
1834 calculateMenu.add(showProducts);
1835 calculateMenu.add(autoCalculate);
1836 calculateMenu.add(sortByTree);
1837 calculateMenu.addSeparator();
1838 calculateMenu.add(extractScores);
1839 webServiceNoServices = new JMenuItem("<No Services>");
1840 webService.add(webServiceNoServices);
1841 pasteMenu.add(pasteNew);
1842 pasteMenu.add(pasteThis);
1843 sort.add(sortIDMenuItem);
1844 sort.add(sortLengthMenuItem);
1845 sort.add(sortGroupMenuItem);
1846 sort.add(sortPairwiseMenuItem);
1847 sort.add(sortByTreeMenu);
1848 calculateTree.add(averageDistanceTreeMenuItem);
1849 calculateTree.add(neighbourTreeMenuItem);
1850 calculateTree.add(avDistanceTreeBlosumMenuItem);
1851 calculateTree.add(njTreeBlosumMenuItem);
1852 jMenu2.add(htmlMenuItem);
1853 jMenu2.add(epsFile);
1854 jMenu2.add(createPNG);
1855 addSequenceMenu.add(addFromFile);
1856 addSequenceMenu.add(addFromText);
1857 addSequenceMenu.add(addFromURL);
1858 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1859 statusPanel.add(statusBar, null);
1860 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1861 jMenu3.add(showAllColumns);
1862 jMenu3.add(showAllSeqs);
1863 jMenu3.add(showAllhidden);
1864 hideMenu.add(hideSelColumns);
1865 hideMenu.add(hideSelSequences);
1866 hideMenu.add(hideAllSelection);
1867 hideMenu.add(hideAllButSelection);
1869 formatMenu.add(font);
1870 formatMenu.addSeparator();
1871 formatMenu.add(wrapMenuItem);
1872 formatMenu.add(scaleAbove);
1873 formatMenu.add(scaleLeft);
1874 formatMenu.add(scaleRight);
1875 formatMenu.add(seqLimits);
1876 formatMenu.add(idRightAlign);
1877 formatMenu.add(hiddenMarkers);
1878 formatMenu.add(viewBoxesMenuItem);
1879 formatMenu.add(viewTextMenuItem);
1880 formatMenu.add(colourTextMenuItem);
1881 formatMenu.add(renderGapsMenuItem);
1882 formatMenu.add(centreColumnLabelsMenuItem);
1883 formatMenu.add(showNonconservedMenuItem);
1884 selectMenu.add(findMenuItem);
1885 selectMenu.addSeparator();
1886 selectMenu.add(selectAllSequenceMenuItem);
1887 selectMenu.add(deselectAllSequenceMenuItem);
1888 selectMenu.add(invertSequenceMenuItem);
1889 selectMenu.add(invertColSel);
1890 selectMenu.add(deleteGroups);
1891 selectMenu.add(grpsFromSelection);
1892 // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
1893 //selectMenu.addSeparator();
1894 //selectMenu.add(listenToViewSelections);
1897 protected void listenToViewSelections_actionPerformed(ActionEvent e)
1899 // TODO Auto-generated method stub
1903 protected void showAllhidden_actionPerformed(ActionEvent e)
1905 // TODO Auto-generated method stub
1909 protected void hideAllButSelection_actionPerformed(ActionEvent e)
1911 // TODO Auto-generated method stub
1915 protected void hideAllSelection_actionPerformed(ActionEvent e)
1917 // TODO Auto-generated method stub
1921 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1923 // TODO Auto-generated method stub
1927 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1929 // TODO Auto-generated method stub
1933 protected void showSequenceLogo_actionPerformed(ActionEvent e)
1935 // TODO Auto-generated method stub
1939 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1941 // TODO Auto-generated method stub
1945 protected void showGroupConsensus_actionPerformed(ActionEvent e)
1947 // TODO Auto-generated method stub
1951 protected void showGroupConservation_actionPerformed(ActionEvent e)
1953 // TODO Auto-generated method stub
1957 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1959 // TODO Auto-generated method stub
1963 protected void showSeqFeaturesHeight_actionPerformed(
1964 ActionEvent actionEvent)
1966 // TODO Auto-generated method stub
1970 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1972 // TODO Auto-generated method stub
1976 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1978 // TODO Auto-generated method stub
1982 protected void followHighlight_actionPerformed()
1984 // TODO Auto-generated method stub
1988 protected void showNpFeats_actionPerformed(ActionEvent e)
1990 // TODO Auto-generated method stub
1994 protected void showDbRefs_actionPerformed(ActionEvent e)
1996 // TODO Auto-generated method stub
2000 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2004 protected void showProducts_actionPerformed(ActionEvent e)
2008 protected void buildSortByAnnotationScoresMenu()
2012 protected void extractScores_actionPerformed(ActionEvent e)
2016 protected void outputText_actionPerformed(ActionEvent e)
2020 public void addFromFile_actionPerformed(ActionEvent e)
2025 public void addFromText_actionPerformed(ActionEvent e)
2030 public void addFromURL_actionPerformed(ActionEvent e)
2035 public void exportFeatures_actionPerformed(ActionEvent e)
2040 public void exportAnnotations_actionPerformed(ActionEvent e)
2045 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2049 protected void closeMenuItem_actionPerformed(boolean b)
2053 protected void redoMenuItem_actionPerformed(ActionEvent e)
2057 protected void undoMenuItem_actionPerformed(ActionEvent e)
2061 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2065 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2069 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2073 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2077 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2081 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2085 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2089 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2093 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2097 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2101 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2105 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2109 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2113 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2117 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2121 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2125 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2129 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2133 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2137 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2141 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2145 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2149 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2153 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2157 protected void clustalColour_actionPerformed(ActionEvent e)
2161 protected void zappoColour_actionPerformed(ActionEvent e)
2165 protected void taylorColour_actionPerformed(ActionEvent e)
2169 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2173 protected void helixColour_actionPerformed(ActionEvent e)
2177 protected void strandColour_actionPerformed(ActionEvent e)
2181 protected void turnColour_actionPerformed(ActionEvent e)
2185 protected void buriedColour_actionPerformed(ActionEvent e)
2189 protected void userDefinedColour_actionPerformed(ActionEvent e)
2193 protected void PIDColour_actionPerformed(ActionEvent e)
2197 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2201 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2205 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2209 protected void printMenuItem_actionPerformed(ActionEvent e)
2213 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2217 protected void findMenuItem_actionPerformed(ActionEvent e)
2221 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2225 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2229 protected void nucleotideColour_actionPerformed(ActionEvent e)
2233 protected void deleteGroups_actionPerformed(ActionEvent e)
2237 protected void copy_actionPerformed(ActionEvent e)
2241 protected void cut_actionPerformed(ActionEvent e)
2245 protected void delete_actionPerformed(ActionEvent e)
2249 protected void pasteNew_actionPerformed(ActionEvent e)
2253 protected void pasteThis_actionPerformed(ActionEvent e)
2257 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2261 public void createPNG(java.io.File f)
2265 protected void font_actionPerformed(ActionEvent e)
2269 protected void seqLimit_actionPerformed(ActionEvent e)
2273 public void seqDBRef_actionPerformed(ActionEvent e)
2278 public void createEPS(java.io.File f)
2282 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2288 * Template method to handle the 'load T-Coffee scores' menu event.
2290 * Subclasses override this method to provide a custom action.
2292 * @param event The raised event
2294 protected void loadScores_actionPerformed(ActionEvent event) {
2300 * Template method to handle the 'Color T-Coffee scores' menu event.
2302 * Subclasses override this method to provide a custom action.
2304 * @param event The raised event
2306 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) {
2311 protected void jpred_actionPerformed(ActionEvent e)
2315 protected void scaleAbove_actionPerformed(ActionEvent e)
2319 protected void scaleLeft_actionPerformed(ActionEvent e)
2323 protected void scaleRight_actionPerformed(ActionEvent e)
2327 protected void modifyPID_actionPerformed(ActionEvent e)
2331 protected void modifyConservation_actionPerformed(ActionEvent e)
2335 protected void saveAs_actionPerformed(ActionEvent e)
2339 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2343 public void vamsasStore_actionPerformed(ActionEvent e)
2348 public void vamsasLoad_actionPerformed(ActionEvent e)
2353 public void showTranslation_actionPerformed(ActionEvent e)
2358 public void featureSettings_actionPerformed(ActionEvent e)
2363 public void fetchSequence_actionPerformed(ActionEvent e)
2368 public void smoothFont_actionPerformed(ActionEvent e)
2373 public void annotationColour_actionPerformed(ActionEvent e)
2378 public void associatedData_actionPerformed(ActionEvent e)
2383 public void autoCalculate_actionPerformed(ActionEvent e)
2388 public void sortByTreeOption_actionPerformed(ActionEvent e)
2393 public void showAllSeqs_actionPerformed(ActionEvent e)
2398 public void showAllColumns_actionPerformed(ActionEvent e)
2403 public void hideSelSequences_actionPerformed(ActionEvent e)
2408 public void hideSelColumns_actionPerformed(ActionEvent e)
2413 public void hiddenMarkers_actionPerformed(ActionEvent e)
2418 public void findPdbId_actionPerformed(ActionEvent e)
2423 public void enterPdbId_actionPerformed(ActionEvent e)
2428 public void pdbFile_actionPerformed(ActionEvent e)
2433 public void invertColSel_actionPerformed(ActionEvent e)
2438 public void tabSelectionChanged(int sel)
2443 public void tabbedPane_mousePressed(MouseEvent e)
2448 public void tabbedPane_focusGained(FocusEvent e)
2453 public void save_actionPerformed(ActionEvent e)
2458 public void reload_actionPerformed(ActionEvent e)
2463 public void newView_actionPerformed(ActionEvent e)
2468 public void textColour_actionPerformed(ActionEvent e)
2473 public void idRightAlign_actionPerformed(ActionEvent e)
2478 public void expandViews_actionPerformed(ActionEvent e)
2483 public void gatherViews_actionPerformed(ActionEvent e)
2488 public void buildTreeMenu()
2493 public void pageSetup_actionPerformed(ActionEvent e)
2498 public void alignmentProperties()