Class WebSequenceDB

    • Constructor Detail

      • WebSequenceDB

        public WebSequenceDB()
    • Method Detail

      • getSequenceFormat

        protected abstract SequenceFormat getSequenceFormat()
      • getAddress

        protected abstract java.net.URL getAddress​(java.lang.String id)
                                            throws java.net.MalformedURLException
        Throws:
        java.net.MalformedURLException
      • getAlphabet

        protected abstract Alphabet getAlphabet()
      • getSequence

        public Sequence getSequence​(java.lang.String id)
                             throws BioException
        Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
        Specified by:
        getSequence in interface SequenceDBLite
        Parameters:
        id - the unique ID
        Returns:
        the matching sequence
        Throws:
        BioException - if the ID is invalid
        BioException - if the io operation times out or has problems connecting. Can also indicate an invalid URL has been constructed.