/**
* Maps sequence positions to the RNA helix they belong to. Key: position,
* Value: helix TODO: Revise or drop in favour of annotation position numbers
/**
* Maps sequence positions to the RNA helix they belong to. Key: position,
* Value: helix TODO: Revise or drop in favour of annotation position numbers
// This loop will find the first rna structure annotation by which to colour
// the sequences.
AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
// This loop will find the first rna structure annotation by which to colour
// the sequences.
AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();