Class ABIFParser

  • Direct Known Subclasses:

    public class ABIFParser
    extends Object
    A general base parser for files produced by ABI software. This includes chromatograms derived from ABI sequencers and potentially other data files as well. The format was described by Clark Tibbetts in his paper "Raw Data File Formats, and the Digital and Analog Raw Data Streams of the ABI PRISM 377 DNA Sequencer." Available online

    Briefly, the format consists of a set of named fixed-length "tagged data records" which may contain data themselves, or pointers to data elsewhere in the file. This class reads these records and exposes them to subclasses through the getDataRecord(java.lang.String, int) method. The attributes of the records as described in Tibbets' paper are exposed through public (final) fields of ABIFParser.TaggedDataRecord instances.

    If a record only contains a pointer to the desired data (see ABIFParser.TaggedDataRecord.hasOffsetData, subclasses may get at the raw data by using ABIFParser.TaggedDataRecord.offsetData:

    This parser provides methods and classes for dealing with the files as streams or local files (local files being more memory-efficient).

    Rhett Sutphin (UI CBCB), Richard Holland