Interface BioEntryDBLite

    • Field Detail

      • BIOENTRYS

        static final ChangeType BIOENTRYS
        Signals that sequences are being added to or remove from the database. The sequences being removed should be listed in the previous field by id, either as a single String, an array or a Set. The sequences being added should be listed in the change field as either an array Object[] { id, seq}, or a Map of id->seq.
    • Method Detail

      • getName

        java.lang.String getName()
        Get the name of this sequence database.
        Returns:
        the name of the sequence database, which may be null.
      • getBioEntry

        BioEntry getBioEntry​(java.lang.String id)
                      throws IllegalIDException,
                             BioException
        Retrieve a single BioEntry by its id.
        Parameters:
        id - the id to retrieve by
        Returns:
        the BioEntry with that id
        Throws:
        IllegalIDException - if the database doesn't know about the id
        BioException - if there was a failure in retrieving the BioEntry
      • getBioEntrys

        BioEntryDB getBioEntrys​(java.util.Set ids,
                                BioEntryDB db)
                         throws BioException,
                                IllegalIDException
        Retrieve multiple BioEntry into a specific sequence database. If that database is null, a new HashBioEntryDB is used.
        Parameters:
        ids - a set of ids to retrieve by
        db - a database to load the seqs into
        Returns:
        the BioEntrys with that id
        Throws:
        IllegalIDException - if the database doesn't know about the id
        BioException