Class INSDseqFormat

  • All Implemented Interfaces:
    SequenceFormat, RichSequenceFormat

    public class INSDseqFormat
    extends RichSequenceFormat.BasicFormat
    Format reader for INSDseq files. This version of INSDseq format will generate and write RichSequence objects. Loosely Based on code from the old, deprecated, object. Understands Does NOT understand the "sites" keyword in INSDReference_position. Interprets this instead as an empty location. This is because there is no obvious way of representing the "sites" keyword in BioSQL. Note also that the INSDInterval tags and associate stuff are not read, as this is duplicate information to the INSDFeature_location tag which is already fully parsed. However, they are written on output, although there is no guarantee that the INSDInterval tags will exactly match the INSDFeature_location tag as it is not possible to exactly reflect its contents using these.
    Alan Li (code based on his work), Richard Holland, George Waldon