Package org.biojava.nbio.structure.domain

Class RemoteDomainProvider

java.lang.Object

org.biojava.nbio.structure.domain.SerializableCache<java.lang.String,java.util.SortedSet<java.lang.String>>

org.biojava.nbio.structure.domain.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 Summary

Fields

Modifier and Type	Field	Description
java.lang.String	url

Fields inherited from class org.biojava.nbio.structure.domain.SerializableCache

cacheFileName, serializedCache

Constructor Summary

Constructors

Constructor	Description
RemoteDomainProvider()
RemoteDomainProvider(boolean cache)	initialize this provider with caching enabled

Method Summary

Modifier and Type	Method	Description
void	flushCache()
java.util.SortedSet<java.lang.String>	getDomainNames(java.lang.String name)	Get a list of constituent domain identifiers
java.util.SortedSet<java.lang.String>	getRepresentativeDomains()	Get the full list of representative domains for the PDB.
static void	main(java.lang.String[] args)

Methods inherited from class org.biojava.nbio.structure.domain.SerializableCache

cache, disableCache, enableCache, get, isCacheEnabled, reloadFromFile

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

main

public static void main(java.lang.String[] args)
                 throws java.io.IOException,
                        StructureException

Throws:

java.io.IOException

StructureException

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