Class RemoteDomainProvider

  • All Implemented Interfaces:
    DomainProvider

    public class RemoteDomainProvider
    extends SerializableCache<java.lang.String,​java.util.SortedSet<java.lang.String>>
    implements DomainProvider
    A DomainProvider that uses a mixture of SCOP and PDP domains. SCOP domains are preferred, with PDP providing a backup for structures where SCOP has not been assigned. As of 2015, this class is equivalent to the method used by RCSB to define representatives for structural similarity comparisons.
    • Field Detail

      • url

        public java.lang.String url
    • Constructor Detail

      • RemoteDomainProvider

        public RemoteDomainProvider()
      • RemoteDomainProvider

        public RemoteDomainProvider​(boolean cache)
                             throws java.io.IOException
        initialize this provider with caching enabled
        Parameters:
        cache -
        Throws:
        java.io.IOException
    • Method Detail

      • getDomainNames

        public java.util.SortedSet<java.lang.String> getDomainNames​(java.lang.String name)
                                                             throws java.io.IOException,
                                                                    StructureException
        Description copied from interface: DomainProvider
        Get a list of constituent domain identifiers
        Specified by:
        getDomainNames in interface DomainProvider
        Parameters:
        name - a structure identifier
        Returns:
        A list of domain names
        Throws:
        java.io.IOException - For IO errors getting the domains
        StructureException - For errors converting name to a valid identifier
      • flushCache

        public void flushCache()
        Overrides:
        flushCache in class SerializableCache<java.lang.String,​java.util.SortedSet<java.lang.String>>
      • getRepresentativeDomains

        public java.util.SortedSet<java.lang.String> getRepresentativeDomains()
                                                                       throws java.io.IOException
        Description copied from interface: DomainProvider
        Get the full list of representative domains for the PDB. The exact definition representatives is implementation-specific, but should cover as many structures as possible.
        Specified by:
        getRepresentativeDomains in interface DomainProvider
        Returns:
        A full list of all representative domains recognized by this provider
        Throws:
        java.io.IOException - For IO errors getting the representatives