Class StockholmFileParser

  • public class StockholmFileParser
    extends Object
    Stockholm file parser.
    for more information about the format refer to
        Compulsory fields:
        AC   Accession number:           Accession number in form PFxxxxx.version or PBxxxxxx.
        ID   Identification:             One word name for family.
        DE   Definition:                 Short description of family.
        AU   Author:                     Authors of the entry.
        SE   Source of seed:             The source suggesting the seed members belong to one family.
        GA   Gathering method:           Search threshold to build the full alignment.
        TC   Trusted Cutoff:             Lowest sequence score and domain score of match in the full alignment.
        NC   Noise Cutoff:               Highest sequence score and domain score of match not in full alignment.
        TP   Type:                       Type of family -- presently Family, Domain, Motif or Repeat.
        SQ   Sequence:                   Number of sequences in alignment.
        //                               End of alignment.
        Optional fields:
        DC   Database Comment:           Comment about database reference.
        DR   Database Reference:         Reference to external database.
        RC   Reference Comment:          Comment about literature reference.
        RN   Reference Number:           Reference Number.
        RM   Reference Medline:          Eight digit medline UI number.
        RT   Reference Title:            Reference Title.
        RA   Reference Author:           Reference Author
        RL   Reference Location:         Journal location.
        PI   Previous identifier:        Record of all previous ID lines.
        KW   Keywords:                   Keywords.
        CC   Comment:                    Comments.
        NE   Pfam accession:             Indicates a nested domain.
        NL   Location:                   Location of nested domains - sequence ID, start and end of insert.
        WK   Wikipedia Reference:        Reference to wikipedia.
        Obsolete fields:
        AL   Alignment method of seed:   The method used to align the seed members.
        AM   Alignment Method:          The order ls and fs hits are aligned to the model to build the full align.
    Amr ALHOSSARY, Marko Vaz