Class GenbankRichSequenceDB

    • Constructor Detail

      • GenbankRichSequenceDB

        public GenbankRichSequenceDB()
        The default constructor delegates to the parent class. The constructor refers to RichObjectFactory.getDefaultNamespace() so make sure your factory is initialised before calling this constructor. Sets the default factory to THRESHOLD.
    • Method Detail

      • makeBatchRequest

        protected String makeBatchRequest​(URL url,
                                          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.
      • getRichSequence

        public RichSequence getRichSequence​(String id,
                                            Namespace nsp)
                                     throws BioException,
                                            IllegalIDException
        Given the appropriate Genbank ID, return the matching RichSequence object. Additionally define a new Namespace for the received RichSequence object.
        Parameters:
        id - the Genbank ID to retrieve.
        nsp - the Namespace to define.
        Returns:
        the matching RichSequence object, or null if not found.
        Throws:
        Exception - if the sequence could not be retrieved for reasons other than the identifier not being found.
        BioException
        IllegalIDException
      • getRichSequences

        public RichSequenceDB getRichSequences​(Set list,
                                               RichSequenceDB database)
                                        throws BioException,
                                               IllegalIDException
        Retrieve rich sequences from a Genbank
        Specified by:
        getRichSequences in interface RichSequenceDBLite
        Parameters:
        list - List of NCBI sequence number (GI), accession, accession.version, fasta or seqid.
        database - Where to store rich sequences. If database is null, use an HashSequenceDB Object.
        Returns:
        The database object with downloaded rich sequences. You will need to cast the sequences you get from this database object into RichSequence objects if you want to access their full features.
        Throws:
        IllegalIDException - if the database doesn't know about the id
        BioException
      • ids

        public Set ids()
        Description copied from interface: SequenceDB
        Get an immutable set of all of the IDs in the database. The ids are legal arguments to getSequence.
        Specified by:
        ids in interface BioEntryDB
        Specified by:
        ids in interface SequenceDB
        Returns:
        a Set of ids - at the moment, strings
      • getNamespace

        public Namespace getNamespace()
        Getter for property namespace.
        Returns:
        Value of property namespace.
      • setNamespace

        public void setNamespace​(Namespace namespace)
        Setter for property namespace.
        Parameters:
        namespace - New value of property namespace.
      • setTool

        public void setTool​(String tool)
        Set the tool identifier for Entrez. Defaults to 'biojavax'.
        Parameters:
        tool - the new identifier.
      • getTool

        public String getTool()
        Get the tool identifier for Entrez. Defaults to 'biojavax'.
        Returns:
        the identifier.
      • setEmail

        public void setEmail​(String email)
        Set the email for Entrez. Defaults to 'anonymous@biojava.org'.
        Parameters:
        email - the new email.
      • getEmail

        public String getEmail()
        Get the email for Entrez. Defaults to 'anonymous@biojava.org'.
        Returns:
        the email.