Class RemoteDomainProvider
- java.lang.Object
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- org.biojava.nbio.structure.domain.SerializableCache<String,SortedSet<String>>
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- org.biojava.nbio.structure.domain.RemoteDomainProvider
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- All Implemented Interfaces:
DomainProvider
public class RemoteDomainProvider extends SerializableCache<String,SortedSet<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.
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Field Summary
Fields Modifier and Type Field Description String
url
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Fields inherited from class org.biojava.nbio.structure.domain.SerializableCache
cacheFileName, serializedCache
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Constructor Summary
Constructors Constructor Description RemoteDomainProvider()
RemoteDomainProvider(boolean cache)
initialize this provider with caching enabled
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
flushCache()
SortedSet<String>
getDomainNames(String name)
Get a list of constituent domain identifiersSortedSet<String>
getRepresentativeDomains()
Get the full list of representative domains for the PDB.static void
main(String[] args)
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Methods inherited from class org.biojava.nbio.structure.domain.SerializableCache
cache, disableCache, enableCache, get, isCacheEnabled, reloadFromFile
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Constructor Detail
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RemoteDomainProvider
public RemoteDomainProvider()
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RemoteDomainProvider
public RemoteDomainProvider(boolean cache) throws IOException
initialize this provider with caching enabled- Parameters:
cache
-- Throws:
IOException
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Method Detail
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getDomainNames
public SortedSet<String> getDomainNames(String name) throws IOException, StructureException
Description copied from interface:DomainProvider
Get a list of constituent domain identifiers- Specified by:
getDomainNames
in interfaceDomainProvider
- Parameters:
name
- a structure identifier- Returns:
- A list of domain names
- Throws:
IOException
- For IO errors getting the domainsStructureException
- For errors converting name to a valid identifier
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main
public static void main(String[] args) throws IOException, StructureException
- Throws:
IOException
StructureException
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flushCache
public void flushCache()
- Overrides:
flushCache
in classSerializableCache<String,SortedSet<String>>
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getRepresentativeDomains
public SortedSet<String> getRepresentativeDomains() throws 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 interfaceDomainProvider
- Returns:
- A full list of all representative domains recognized by this provider
- Throws:
IOException
- For IO errors getting the representatives
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