private JMenuItem justifyLeftMenuItem=new JMenuItem();
private JMenuItem justifyRightMenuItem=new JMenuItem();
-
+
+ JMenu autoAnnMenu = new JMenu();
+ protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showConsensusHistogram=new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showSequenceLogo=new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem();
+
+ private JMenuItem grpsFromSelection = new JMenuItem();
public GAlignFrame()
{
try
invertSequenceMenuItem_actionPerformed(e);
}
});
+ grpsFromSelection.setText("Make Groups for selection");
+ grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ makeGrpsFromSelection_actionPerformed(e);
+ }
+ });
+
remove2LeftMenuItem.setText("Remove Left");
remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
showSeqFeatures_actionPerformed(actionEvent);
}
});
- showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
+/*
+ * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
showSeqFeaturesHeight.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
{
showSeqFeaturesHeight_actionPerformed(actionEvent);
}
- });
+ }); */
showDbRefsMenuitem.setText("Show Database Refs");
showDbRefsMenuitem.addActionListener(new ActionListener()
{
}
});
+ showGroupConservation.setText("Group Conservation");
+ showGroupConservation.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showGroupConservation_actionPerformed(e);
+ }
+
+ });
+
+ showGroupConsensus.setText("Group Consensus");
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showGroupConsensus_actionPerformed(e);
+ }
+
+ });
+ showConsensusHistogram.setText("Show Consensus Histogram");
+ showConsensusHistogram.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showConsensusHistogram_actionPerformed(e);
+ }
+
+ });
+ showSequenceLogo.setText("Show Consensus Logo");
+ showSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showSequenceLogo_actionPerformed(e);
+ }
+
+ });
+ applyAutoAnnotationSettings.setText("Apply to all groups");
+ applyAutoAnnotationSettings.setState(false);
+ applyAutoAnnotationSettings.setVisible(true);
+ applyAutoAnnotationSettings.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ applyAutoAnnotationSettings_actionPerformed(e);
+ }
+
+ });
+
nucleotideColour.setText("Nucleotide");
nucleotideColour.addActionListener(new java.awt.event.ActionListener()
{
}
});
tooltipSettingsMenu.setText("Sequence ID Tooltip");
+ autoAnnMenu.setText("Autocalculated Annotation");
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
viewMenu.addSeparator();
viewMenu.add(followHighlightMenuItem);
viewMenu.add(annotationPanelMenuItem);
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ viewMenu.add(autoAnnMenu);
viewMenu.addSeparator();
viewMenu.add(showSeqFeatures);
- viewMenu.add(showSeqFeaturesHeight);
+ //viewMenu.add(showSeqFeaturesHeight);
viewMenu.add(featureSettings);
tooltipSettingsMenu.add(showDbRefsMenuitem);
selectMenu.add(invertSequenceMenuItem);
selectMenu.add(invertColSel);
selectMenu.add(deleteGroups);
+ selectMenu.add(grpsFromSelection);
+ }
+
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showGroupConservation_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
}
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)