Class CachedRemoteScopInstallation

  • All Implemented Interfaces:
    ScopDatabase

    public class CachedRemoteScopInstallation
    extends SerializableCache<java.lang.String,​ScopDomain>
    implements ScopDatabase
    An extension of the RemoteScopInstallation that caches some of the data locally.
    Author:
    Andreas Prlic
    • Constructor Detail

      • CachedRemoteScopInstallation

        public CachedRemoteScopInstallation()
                                     throws java.io.IOException
        Throws:
        java.io.IOException
      • CachedRemoteScopInstallation

        public CachedRemoteScopInstallation​(boolean useCache)
                                     throws java.io.IOException
        Throws:
        java.io.IOException
    • Method Detail

      • getByCategory

        public java.util.List<ScopDescription> getByCategory​(ScopCategory category)
        Description copied from interface: ScopDatabase
        Get all records of a particular classification.
        Specified by:
        getByCategory in interface ScopDatabase
        Parameters:
        category - e.g. "superfamily"
        Returns:
        all records of this type
      • filterByClassificationId

        public java.util.List<ScopDescription> filterByClassificationId​(java.lang.String query)
        Description copied from interface: ScopDatabase
        Get all scop descriptions that start with a classification ID, e.g. b.1.18
        Specified by:
        filterByClassificationId in interface ScopDatabase
        Returns:
        list of scop descriptions
      • getTree

        public java.util.List<ScopNode> getTree​(ScopDomain domain)
        Description copied from interface: ScopDatabase
        get the SCOP sub-tree for a particular domain.
        Specified by:
        getTree in interface ScopDatabase
        Returns:
        list of ScopNodes providing the path to this domain
      • filterByDomainName

        public java.util.List<ScopDomain> filterByDomainName​(java.lang.String query)
        Description copied from interface: ScopDatabase
        search through SCOP and filter based on domain name
        Specified by:
        filterByDomainName in interface ScopDatabase
        Parameters:
        query - a (part) of a name
        Returns:
        list of matchin ScopDomains
      • filterByDescription

        public java.util.List<ScopDescription> filterByDescription​(java.lang.String query)
        Description copied from interface: ScopDatabase
        Get all scop descriptions that start with a certain name. e.g. Globin
        Specified by:
        filterByDescription in interface ScopDatabase
        Returns:
        list of scop descriptions
      • getDomainsForPDB

        public java.util.List<ScopDomain> getDomainsForPDB​(java.lang.String pdbId)
        Description copied from interface: ScopDatabase
        Get a list of ScopDomains that have been assigned to a PDB ID
        Specified by:
        getDomainsForPDB in interface ScopDatabase
        Parameters:
        pdbId - the PDB entry
        Returns:
        a list of ScopDomains
      • getDomainByScopID

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

        public ScopNode getScopNode​(int sunid)
        Description copied from interface: ScopDatabase
        Access a particular ScopNode. The scopNode then allows to traverse through the scop hierarchy...
        Specified by:
        getScopNode in interface ScopDatabase
        Parameters:
        sunid - the scop unique id
        Returns:
        a ScopNode that matches this sunid
      • getScopVersion

        public java.lang.String getScopVersion()
        Description copied from interface: ScopDatabase
        Returns the SCOP version
        Specified by:
        getScopVersion in interface ScopDatabase
        Returns:
        version of SCOP
      • setScopVersion

        public void setScopVersion​(java.lang.String version)
        Description copied from interface: ScopDatabase
        Sets the scop version used.
        Specified by:
        setScopVersion in interface ScopDatabase
      • getScopDomainsBySunid

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

        public java.util.List<java.lang.String> getComments​(int sunid)
        Description copied from interface: ScopDatabase
        Get comments about a SCOP domain by its sunid
        Specified by:
        getComments in interface ScopDatabase
        Returns: