org.biojava.nbio.structure.domain

Class RemotePDPProvider

java.lang.Object

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

org.biojava.nbio.structure.domain.RemotePDPProvider

All Implemented Interfaces:

PDPProvider

public class RemotePDPProvider
extends SerializableCache<String,SortedSet<String>>
implements PDPProvider

A class that provided PDP assignments that are loaded from a remote web server

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_SERVER

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

cacheFileName, serializedCache

Constructor Summary

Constructors

Constructor and Description
RemotePDPProvider()
RemotePDPProvider(boolean useCache)

Method Summary

Modifier and Type	Method and Description
Structure	getDomain(String pdpDomainName, AtomCache cache) Get the structure for a particular PDP domain
PDPDomain	getPDPDomain(String pdpDomainName) Get a StructureIdentifier representing the specified PDP domain.
SortedSet<String>	getPDPDomainNamesForPDB(String pdbId) Get a list of all PDP domains for a given PDB entry
String	getServer()
static void	main(String[] args)
void	setServer(String server)

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

cache, disableCache, enableCache, flushCache, get, isCacheEnabled, reloadFromFile

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

RemotePDPProvider

public RemotePDPProvider()

RemotePDPProvider

public RemotePDPProvider(boolean useCache)
                  throws IOException

Parameters:

useCache -

Throws:

IOException

Method Detail

main

public static void main(String[] args)
                 throws IOException,
                        StructureException

Throws:

IOException

StructureException

getServer

public String getServer()

setServer

public void setServer(String server)

getDomain

public Structure getDomain(String pdpDomainName,
                           AtomCache cache)
                    throws IOException,
                           StructureException

Get the structure for a particular PDP domain

Specified by:

getDomain in interface PDPProvider

Parameters:

pdpDomainName - PDP identifier, e.g. "PDP:4HHBAa"

cache - AtomCache, responsible for fetching and storing the coordinates

Returns:

Structure representing the PDP domain

Throws:

IOException - if the server cannot be reached

StructureException - For errors parsing the structure

getPDPDomain

public PDPDomain getPDPDomain(String pdpDomainName)
                       throws IOException

Get a StructureIdentifier representing the specified PDP domain.

Specified by:

getPDPDomain in interface PDPProvider

Parameters:

pdpDomainName - PDP domain name

Returns:

a PDPDomain representing this domain name

Throws:

IOException - if the server cannot be reached

getPDPDomainNamesForPDB

public SortedSet<String> getPDPDomainNamesForPDB(String pdbId)
                                          throws IOException

Get a list of all PDP domains for a given PDB entry

Specified by:

getPDPDomainNamesForPDB in interface PDPProvider

Parameters:

pdbId - PDB ID

Returns:

Set of domain names, e.g. "PDP:4HHBAa"

Throws:

IOException - if the server cannot be reached