Package org.biojava.nbio.structure.scop

Class CachedRemoteScopInstallation

java.lang.Object

org.biojava.nbio.structure.domain.SerializableCache<String,ScopDomain>

org.biojava.nbio.structure.scop.CachedRemoteScopInstallation

All Implemented Interfaces:

ScopDatabase

public class CachedRemoteScopInstallation
extends SerializableCache<String,ScopDomain>
implements ScopDatabase

An extension of the RemoteScopInstallation that caches some of the data locally.

Author:

Andreas Prlic

Field Summary

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

cacheFileName, serializedCache

Constructor Summary

Constructors

Constructor	Description
CachedRemoteScopInstallation()
CachedRemoteScopInstallation(boolean useCache)

Method Summary

Modifier and Type	Method	Description
List<ScopDescription>	filterByClassificationId(String query)	Get all scop descriptions that start with a classification ID, e.g. b.1.18
List<ScopDescription>	filterByDescription(String query)	Get all scop descriptions that start with a certain name. e.g.
List<ScopDomain>	filterByDomainName(String query)	search through SCOP and filter based on domain name
void	flushCache()
List<ScopDescription>	getByCategory(ScopCategory category)	Get all records of a particular classification.
List<String>	getComments(int sunid)	Get comments about a SCOP domain by its sunid
ScopDomain	getDomainByScopID(String scopId)	get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
List<ScopDomain>	getDomainsForPDB(String pdbId)	Get a list of ScopDomains that have been assigned to a PDB ID
ScopDescription	getScopDescriptionBySunid(int sunid)	Return the SCOP description for a node in the hierarchy by its "sunid" id.
List<ScopDomain>	getScopDomainsBySunid(Integer sunid)	Get a SCOP domain by its sunid
ScopNode	getScopNode(int sunid)	Access a particular ScopNode.
String	getScopVersion()	Returns the SCOP version
List<ScopNode>	getTree(ScopDomain domain)	get the SCOP sub-tree for a particular domain.
void	setScopVersion(String version)	Sets the scop version used.

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

Constructor Detail

CachedRemoteScopInstallation

public CachedRemoteScopInstallation()
                             throws IOException

Throws:

IOException

CachedRemoteScopInstallation

public CachedRemoteScopInstallation(boolean useCache)
                             throws IOException

Throws:

IOException

Method Detail

getByCategory

public 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 List<ScopDescription> filterByClassificationId(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 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 List<ScopDomain> filterByDomainName(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 List<ScopDescription> filterByDescription(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

getScopDescriptionBySunid

public ScopDescription getScopDescriptionBySunid(int sunid)

Description copied from interface: ScopDatabase

Return the SCOP description for a node in the hierarchy by its "sunid" id.

Specified by:

getScopDescriptionBySunid in interface ScopDatabase

Returns:

a ScopDescription object

getDomainsForPDB

public List<ScopDomain> getDomainsForPDB(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(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 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(String version)

Description copied from interface: ScopDatabase

Sets the scop version used.

Specified by:

setScopVersion in interface ScopDatabase

getScopDomainsBySunid

public List<ScopDomain> getScopDomainsBySunid(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

flushCache

public void flushCache()

Overrides:

flushCache in class SerializableCache<String,ScopDomain>

getComments

public List<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: