Interface ScopDatabase

Method Details

• getByCategory

  List<ScopDescription> getByCategory(ScopCategory category)

  Get all records of a particular classification.

  Parameters:

  category - e.g. "superfamily"

  Returns:

  all records of this type

• filterByClassificationId

  List<ScopDescription> filterByClassificationId(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

  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

  List<ScopDomain> filterByDomainName(String query)

  search through SCOP and filter based on domain name

  Parameters:

  query - a (part) of a name

  Returns:

  list of matchin ScopDomains

• filterByDescription

  List<ScopDescription> filterByDescription(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

  List<ScopDomain> getDomainsForPDB(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(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

  String getScopVersion()

  Returns the SCOP version

  Returns:

  version of SCOP

• setScopVersion

  void setScopVersion(String version)

  Sets the scop version used.

  Parameters:

  version -

  Throws:

  UnsupportedOperationException - If the version cannot be changed

• getScopDomainsBySunid

  List<ScopDomain> getScopDomainsBySunid(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

  List<String> getComments(int sunid)

  Get comments about a SCOP domain by its sunid

  Parameters:

  sunid -

  Returns: