Working with annotations

An annotation is anything that can be represented as a genomic interval. An annotation

• is found on a particular chromosome or reference
• has a start coordinate
• has an end coordinate
• is either positive-stranded, negative-stranded, or double-stranded

Previous versions of the codebase made a distinction between a SingleInterval, representing a single continuous genomic block, and a BlockedAnnotation, composed of multiple blocks or exons. The current codebase eliminates this distinction. An Annotated object represents any number of genomic blocks or exons, provided that they all belong to the same reference and are on the same strand.

Making an annotation with one block is straightforward:

Annotated annot = new Annotation("chr1", 3000, 4000, Strand.POSITIVE);