import jalview.analysis.GeneticCodes;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+@SuppressWarnings("serial")
public class GAlignFrame extends JInternalFrame
{
protected JMenuBar alignFrameMenuBar = new JMenuBar();
protected JMenuItem closeMenuItem = new JMenuItem();
- protected JMenu webService = new JMenu();
+ public JMenu webService = new JMenu();// BH 2019 was protected, but not
+ // sufficient for AlignFrame thread run
- protected JMenuItem webServiceNoServices;
+ public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
+ // sufficient for AlignFrame thread run
protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
protected JMenu sortByAnnotScore = new JMenu();
- protected JLabel statusBar = new JLabel();
+ public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
+ // sufficient for
+ // AlignFrame.printWriter
protected JMenu outputTextboxMenu = new JMenu();
protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
- protected JTabbedPane tabbedPane = jalview.jbgui.GDesktop.createTabbedPane();
+ protected JTabbedPane tabbedPane = new JTabbedPane();
protected JMenuItem reload = new JMenuItem();
protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
-
+
protected JMenuItem openFeatureSettings;
private SequenceAnnotationOrder annotationSortOrder;
{
try
{
+
+ // for Web-page embedding using id=align-frame-div
+ setName(Jalview.getAppID("alignment"));
+
jbInit();
setJMenuBar(alignFrameMenuBar);
this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setBackground(Color.white);
+ // statusBar.setBackground(Color.white); BH 2019.08.01 -- this does nothing,
+ // as the label is not opaque
+ statusBar.setOpaque(true);// BH 2019.07.01 -- setting a label opaque avoids
+ // frame repaint in SwingJS and has no effect in
+ // Java
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText(MessageManager.getString("label.status_bar"));
annotationPanelMenuItem
.setText(MessageManager.getString("label.show_annotations"));
annotationPanelMenuItem
- .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
+ .setState(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true));
annotationPanelMenuItem.addActionListener(new ActionListener()
{
@Override
});
seqLimits.setText(
MessageManager.getString("label.show_sequence_limits"));
- seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+ seqLimits.setState(jalview.bin.Cache.getDefault(Preferences.SHOW_JVSUFFIX, true));
seqLimits.addActionListener(new ActionListener()
{
@Override
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
padGapsMenuitem
- .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ .setState(jalview.bin.Cache.getDefault(Preferences.PAD_GAPS, false));
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
/*
* Translate as cDNA with sub-menu of translation tables
*/
- showTranslation.setText(MessageManager
- .getString("label.translate_cDNA"));
+ showTranslation
+ .setText(MessageManager.getString("label.translate_cDNA"));
boolean first = true;
- for (final GeneticCodeI table : GeneticCodes.getInstance()
- .getCodeTables())
+ for (final GeneticCodeI table : GeneticCodes.getCodeTables())
{
JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
showTranslation.add(item);
associatedData_actionPerformed(e);
}
});
- loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
+ loadVcf = new JMenuItem(
+ MessageManager.getString("label.load_vcf_file"));
loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
loadVcf.addActionListener(new ActionListener()
{
autoCalculate.setText(
MessageManager.getString("label.autocalculate_consensus"));
autoCalculate.setState(
- jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ jalview.bin.Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
sortByTree.setToolTipText("<html>" + MessageManager.getString(
"label.enable_automatically_sort_alignment_when_open_new_tree"));
sortByTree
- .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+ .setState(jalview.bin.Cache.getDefault(Preferences.SORT_BY_TREE,
+ false));
sortByTree.addActionListener(new ActionListener()
{
@Override