Interface ScopDatabase

    • Method Detail

      • getByCategory

        java.util.List<ScopDescription> getByCategory​(ScopCategory category)
        Get all records of a particular classification.
        Parameters:
        category - e.g. "superfamily"
        Returns:
        all records of this type
      • filterByClassificationId

        java.util.List<ScopDescription> filterByClassificationId​(java.lang.String query)
        Get all scop descriptions that start with a classification ID, e.g. b.1.18
        Parameters:
        query -
        Returns:
        list of scop descriptions
      • getTree

        java.util.List<ScopNode> getTree​(ScopDomain domain)
        get the SCOP sub-tree for a particular domain.
        Parameters:
        domain -
        Returns:
        list of ScopNodes providing the path to this domain
      • filterByDomainName

        java.util.List<ScopDomain> filterByDomainName​(java.lang.String query)
        search through SCOP and filter based on domain name
        Parameters:
        query - a (part) of a name
        Returns:
        list of matchin ScopDomains
      • filterByDescription

        java.util.List<ScopDescription> filterByDescription​(java.lang.String query)
        Get all scop descriptions that start with a certain name. e.g. Globin
        Parameters:
        query -
        Returns:
        list of scop descriptions
      • getScopDescriptionBySunid

        ScopDescription getScopDescriptionBySunid​(int sunid)
        Return the SCOP description for a node in the hierarchy by its "sunid" id.
        Parameters:
        sunid -
        Returns:
        a ScopDescription object
      • getDomainsForPDB

        java.util.List<ScopDomain> getDomainsForPDB​(java.lang.String pdbId)
        Get a list of ScopDomains that have been assigned to a PDB ID
        Parameters:
        pdbId - the PDB entry
        Returns:
        a list of ScopDomains
      • getDomainByScopID

        ScopDomain getDomainByScopID​(java.lang.String scopId)
        get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
        Parameters:
        scopId - e.g. d2bq6a1
        Returns:
        a ScopDomain or null if no domain with the particular ID could be found
      • getScopNode

        ScopNode getScopNode​(int sunid)
        Access a particular ScopNode. The scopNode then allows to traverse through the scop hierarchy...
        Parameters:
        sunid - the scop unique id
        Returns:
        a ScopNode that matches this sunid
      • getScopVersion

        java.lang.String getScopVersion()
        Returns the SCOP version
        Returns:
        version of SCOP
      • setScopVersion

        void setScopVersion​(java.lang.String version)
        Sets the scop version used.
        Parameters:
        version -
        Throws:
        java.lang.UnsupportedOperationException - If the version cannot be changed
      • getScopDomainsBySunid

        java.util.List<ScopDomain> getScopDomainsBySunid​(java.lang.Integer sunid)
        Get a SCOP domain by its sunid
        Parameters:
        sunid - the scop unique id
        Returns:
        a list of scop domains that match this sunid
      • getComments

        java.util.List<java.lang.String> getComments​(int sunid)
        Get comments about a SCOP domain by its sunid
        Parameters:
        sunid -
        Returns: