org.biojava.bio.structure.scop
Class RemoteScopInstallation

java.lang.Object
  extended by org.biojava.bio.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
static String DEFAULT_SERVER
           
 
Constructor Summary
RemoteScopInstallation()
           
 
Method Summary
 List<ScopDescription> filterByClassificationId(String query)
          Get all scop descriptions that start with a classifcation 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.
 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 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 classifcation 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

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