RemoteDomainProvider

java.lang.Object
- org.biojava.nbio.structure.domain.SerializableCache<java.lang.String,java.util.SortedSet<java.lang.String>>
- - org.biojava.nbio.structure.domain.RemoteDomainProvider

All Implemented Interfaces:

DomainProvider
```
public class RemoteDomainProvider
extends SerializableCache<java.lang.String,java.util.SortedSet<java.lang.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.

Field Summary

Fields
Modifier and Type Field and Description

java.lang.String url
- Fields inherited from class org.biojava.nbio.structure.domain.SerializableCache
  cacheFileName, serializedCache

Fields
Modifier and Type	Field and Description
`java.lang.String`	`url`

Constructor Summary

Constructors
Constructor and Description

RemoteDomainProvider()

RemoteDomainProvider(boolean cache)
initialize this provider with caching enabled

Constructors
Constructor and Description
`RemoteDomainProvider()`
`RemoteDomainProvider(boolean cache)` initialize this provider with caching enabled

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`flushCache()`
`java.util.SortedSet<java.lang.String>`	`getDomainNames(java.lang.String name)` Get a list of constituent domain identifiers
`java.util.SortedSet<java.lang.String>`	`getRepresentativeDomains()` Get the full list of representative domains for the PDB.
`static void`	`main(java.lang.String[] args)`

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

- Field Detail
  - url
```
public java.lang.String url
```
- Constructor Detail
  - RemoteDomainProvider
```
public RemoteDomainProvider()
```
  - RemoteDomainProvider
```
public RemoteDomainProvider(boolean cache)
                     throws java.io.IOException
```
    initialize this provider with caching enabled
    
    Parameters:
    
    cache -
    
    Throws:
    
    java.io.IOException
- Method Detail
  - getDomainNames
```
public java.util.SortedSet<java.lang.String> getDomainNames(java.lang.String name)
                                                     throws java.io.IOException,
                                                            StructureException
```
    Description copied from interface: DomainProvider
    
    Get a list of constituent domain identifiers
    
    Specified by:
    
    getDomainNames in interface DomainProvider
    
    Parameters:
    
    name - a structure identifier
    
    Returns:
    
    A list of domain names
    
    Throws:
    
    java.io.IOException - For IO errors getting the domains
    
    StructureException - For errors converting name to a valid identifier
  - main
```
public static void main(java.lang.String[] args)
                 throws java.io.IOException,
                        StructureException
```
    Throws:
    
    java.io.IOException
    
    StructureException
  - flushCache
```
public void flushCache()
```
    Overrides:
    
    flushCache in class SerializableCache<java.lang.String,java.util.SortedSet<java.lang.String>>
  - getRepresentativeDomains
```
public java.util.SortedSet<java.lang.String> getRepresentativeDomains()
                                                               throws java.io.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 interface DomainProvider
    
    Returns:
    
    A full list of all representative domains recognized by this provider
    
    Throws:
    
    java.io.IOException - For IO errors getting the representatives

Class RemoteDomainProvider

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

url

Constructor Detail

RemoteDomainProvider

RemoteDomainProvider

Method Detail

getDomainNames

main

flushCache

getRepresentativeDomains