import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
import jalview.io.SequenceAnnotationReport;
-import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
add(menuItem);
}
-
}
SequenceGroup sg = ap.av.getSelectionGroup();
ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
+ conservationMenuItem.setEnabled(!sg.isNucleotide());
+
if (sg.cs != null)
{
if (sg.cs.conservationApplied())
hideInsertions_actionPerformed(e);
}
});
- /*
- * annotationMenuItem.setText("By Annotation");
- * annotationMenuItem.addActionListener(new ActionListener() { public void
- * actionPerformed(ActionEvent actionEvent) {
- * annotationMenuItem_actionPerformed(actionEvent); } });
- */
+
groupMenu.add(sequenceSelDetails);
add(groupMenu);
add(sequenceMenu);
@Override
public void actionPerformed(ActionEvent e)
{
- abovePIDColour_actionPerformed();
+ abovePIDColour_actionPerformed(abovePIDColour.isSelected());
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- conservationMenuItem_actionPerformed();
+ conservationMenuItem_actionPerformed(conservationMenuItem
+ .isSelected());
}
});
/**
* DOCUMENT ME!
*
+ * @param selected
+ *
* @param e
* DOCUMENT ME!
*/
- protected void abovePIDColour_actionPerformed()
+ public void abovePIDColour_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
return;
}
- boolean selected = abovePIDColour.isSelected();
if (selected)
{
sg.cs.setConsensus(AAFrequency.calculate(
* @param e
* DOCUMENT ME!
*/
- protected void conservationMenuItem_actionPerformed()
+ public void conservationMenuItem_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
return;
}
- boolean selected = conservationMenuItem.isSelected();
if (selected)
{
// JBPNote: Conservation name shouldn't be i18n translated
refresh();
}
- public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
- {
- SequenceGroup sg = getGroup();
- if (sg == null)
- {
- return;
- }
-
- AnnotationColourGradient acg = new AnnotationColourGradient(
- sequence.getAnnotation()[0], null,
- AnnotationColourGradient.NO_THRESHOLD);
-
- acg.setPredefinedColours(true);
- sg.setColourScheme(acg);
-
- refresh();
- }
-
/**
* DOCUMENT ME!
*
/**
* Action on user selecting an item from the colour menu (that does not have
* its bespoke action handler)
+ *
+ * @return
*/
@Override
public void changeColour_actionPerformed(String colourSchemeName)