oldgroupColours = new Hashtable();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- if (sg.cs != null)
+ if (sg.getColourScheme() != null)
{
- oldgroupColours.put(sg, sg.cs);
+ oldgroupColours.put(sg, sg.getColourScheme());
}
else
{
AnnotationColourGradient acg = null;
if (currentColours.getState())
{
- acg = new AnnotationColourGradient(currentAnnotation,
- av.getGlobalColourScheme(), aboveThreshold);
}
else
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- if (sg.cs == null)
+ if (sg.getColourScheme() == null)
{
continue;
}
if (currentColours.getState())
{
- sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
- aboveThreshold);
+ sg.setColourScheme(new AnnotationColourGradient(
+ currentAnnotation, sg.getColourScheme(), aboveThreshold));
}
else
{
- sg.cs = new AnnotationColourGradient(currentAnnotation,
- minColour.getBackground(), maxColour.getBackground(),
- aboveThreshold);
+ sg.setColourScheme(new AnnotationColourGradient(
+ currentAnnotation, minColour.getBackground(), maxColour
+ .getBackground(), aboveThreshold));
}
}
Object cs = oldgroupColours.get(sg);
if (cs instanceof ColourSchemeI)
{
- sg.cs = (ColourSchemeI) cs;
+ sg.setColourScheme((ColourSchemeI) cs);
}
else
{
// probably the "null" string we set it to if it was null originally.
- sg.cs = null;
+ sg.setColourScheme(null);
}
}
}