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
    • Method Detail

      • getDataBase

        public java.lang.String getDataBase()
      • setDatabase

        public void setDatabase​(java.lang.String dataBase)
                         throws BioException
        Parameters:
        dataBase - must be one of "nucleotide" or "protein" (use the static DB fields)
        Throws:
        BioException - if an unknown database name is used.
      • setSequenceFormat

        public void setSequenceFormat​(SequenceFormat format)
                               throws BioException
        Parameters:
        format - must be one of FastaFormat or GenbankFormat
        Throws:
        BioException - if an unknown SequenceFormat is used
      • getAddress

        protected java.net.URL getAddress​(java.lang.String uid)
                                   throws java.net.MalformedURLException
        Specified by:
        getAddress in class WebSequenceDB
        Throws:
        java.net.MalformedURLException
      • getName

        public java.lang.String getName()
        Description copied from interface: SequenceDBLite
        Get the name of this sequence database.
        Returns:
        the name of the sequence database, which may be null.