org.biojava.nbio.structure.domain

Interface DomainProvider

All Known Implementing Classes:

PDBDomainProvider, RemoteDomainProvider

public interface DomainProvider

Decomposes a structure from the PDB into representative domains

Method Summary

Modifier and Type	Method and Description
SortedSet<String>	getDomainNames(String name) Get a list of constituent domain identifiers
SortedSet<String>	getRepresentativeDomains() Get the full list of representative domains for the PDB.

Method Detail

getDomainNames

SortedSet<String> getDomainNames(String name)
                          throws IOException,
                                 StructureException

Get a list of constituent domain identifiers

Parameters:

name - a structure identifier

Returns:

A list of domain names

Throws:

IOException - For IO errors getting the domains

StructureException - For errors converting name to a valid identifier

getRepresentativeDomains

SortedSet<String> getRepresentativeDomains()
                                    throws IOException

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.

Returns:

A full list of all representative domains recognized by this provider

Throws:

IOException - For IO errors getting the representatives