Class GenbankSequenceDB


  • public class GenbankSequenceDB
    extends java.lang.Object
    This class contains functions accessing DNA sequences in Genbank format.
    Author:
    Lei Lai, Matthew Pocock, Laurent Jourdren, Shuvankar Mukherjee, Mark Schreiber, Richard Holland
    • Method Detail

      • getAddress

        protected java.net.URL getAddress​(java.lang.String id)
                                   throws java.net.MalformedURLException
        Get the URL object for locating sequence object using eutils. The default value of the return format of the sequence object is text.
        Throws:
        java.net.MalformedURLException
      • getAddress

        protected java.net.URL getAddress​(java.lang.String id,
                                          java.lang.String format)
                                   throws java.net.MalformedURLException
        Get the URL object for locating sequence object using eutils. User could specify the return format of the sequence object.
        Throws:
        java.net.MalformedURLException
      • getName

        public java.lang.String getName()
      • getSequence

        public Sequence getSequence​(java.lang.String id)
                             throws java.lang.Exception
        Throws:
        java.lang.Exception
      • makeBatchRequest

        protected java.lang.String makeBatchRequest​(java.net.URL url,
                                                    java.util.Set list)
        Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank.
        Parameters:
        url - URL of the request
        list - List of sequence identifier
        Returns:
        The Post request.
      • getSequences

        public SequenceDB getSequences​(java.util.Set list)
                                throws BioException
        Retrieve sequences from a Genbank
        Parameters:
        list - List of NCBI sequence number (GI), accession, accession.version, fasta or seqid.
        Returns:
        The database object (HashSequenceDB) with downloaded sequences.
        Throws:
        BioException
      • getSequences

        public SequenceDB getSequences​(java.util.Set list,
                                       SequenceDB database)
                                throws BioException
        Retrieve sequences from a Genbank
        Parameters:
        list - List of NCBI sequence number (GI), accession, accession.version, fasta or seqid.
        database - Where to store sequences. if database is null, use an HashSequenceDB Objet.
        Returns:
        The database object with downloaded sequences.
        Throws:
        BioException