Class NCBISequenceDB

    • Constructor Detail

      • NCBISequenceDB

        public NCBISequenceDB()
        Default constructor, querys the Genbank nucleotide database on "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi" and retrieves sequences in FastaFormat.
      • NCBISequenceDB

        public NCBISequenceDB​(java.lang.String database,
                              SequenceFormat format)
        Parameterized constructor
        Parameters:
        database - must be one of "nucleotide" or "protein" (use the static DB fields)
        format - must be one of GenbankFormat or FastaFormat
        Throws:
        BioRuntimeException - if the database or format is invalid
      • NCBISequenceDB

        public NCBISequenceDB​(java.lang.String server,
                              java.lang.String CGI,
                              java.lang.String database,
                              SequenceFormat format)
                       throws BioRuntimeException
        Parameterized constructor
        Parameters:
        server - eg "http://www.ncbi.nlm.nih.gov/"
        CGI - eg "entrez/query.fcgi"
        database - must be one of "nucleotide" or "protein" (use the static DB fields)
        format - must be one of GenbankFormat or FastaFormat
        Throws:
        BioRuntimeException - if the database or format is invalid