org.biojava.nbio.structure.scop

Class RemoteScopInstallation

java.lang.Object

org.biojava.nbio.structure.scop.RemoteScopInstallation

All Implemented Interfaces:

ScopDatabase

public class RemoteScopInstallation
extends Object
implements ScopDatabase

A class that fetches information about SCOP from a remote data-source. It requires port 80 to open for HTTP connection.

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_SERVER

Constructor Summary

Constructors

Constructor and Description
RemoteScopInstallation()

Method Summary

Methods

Modifier and Type	Method and Description
List<ScopDescription>	filterByClassificationId(String query) Get all scop descriptions that start with a classification ID, e.g.
List<ScopDescription>	filterByDescription(String query) Get all scop descriptions that start with a certain name.
List<ScopDomain>	filterByDomainName(String query) search through SCOP and filter based on domain name
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
String	getServer()
List<ScopNode>	getTree(ScopDomain domain) get the SCOP sub-tree for a particular domain.
static void	main(String[] args)
void	setScopVersion(String version) Sets the scop version used.
void	setServer(String server)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_SERVER

public static final String DEFAULT_SERVER

See Also:

Constant Field Values

Constructor Detail

RemoteScopInstallation

public RemoteScopInstallation()

Method Detail

main

public static void main(String[] args)

getServer

public String getServer()

setServer

public void setServer(String server)

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

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: