RemotePDPProvider

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

All Implemented Interfaces:: PDPProvider

public class RemotePDPProvider
extends SerializableCache<java.lang.String,java.util.SortedSet<java.lang.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 Description

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

Fields
Modifier and Type	Field	Description
`static java.lang.String`	`DEFAULT_SERVER`

Constructor Summary

Constructors
Constructor Description

RemotePDPProvider()

RemotePDPProvider(boolean useCache)

Constructors
Constructor	Description
`RemotePDPProvider()`
`RemotePDPProvider(boolean useCache)`

Method Summary

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from class org.biojava.nbio.structure.domain.SerializableCache
cache, disableCache, enableCache, flushCache, get, isCacheEnabled, reloadFromFile

- Field Detail
  - DEFAULT_SERVER
```
public static final java.lang.String DEFAULT_SERVER
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - RemotePDPProvider
```
public RemotePDPProvider()
```
  - RemotePDPProvider
```
public RemotePDPProvider(boolean useCache)
                  throws java.io.IOException
```
    Parameters:
    
    useCache -
    
    Throws:
    
    java.io.IOException
- Method Detail
  - main
```
public static void main(java.lang.String[] args)
                 throws java.io.IOException,
                        StructureException
```
    Throws:
    
    java.io.IOException
    
    StructureException
  - getServer
```
public java.lang.String getServer()
```
  - setServer
```
public void setServer(java.lang.String server)
```
  - getDomain
```
public Structure getDomain(java.lang.String pdpDomainName,
                           AtomCache cache)
                    throws java.io.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:
    
    java.io.IOException - if the server cannot be reached
    
    StructureException - For errors parsing the structure
  - getPDPDomain
```
public PDPDomain getPDPDomain(java.lang.String pdpDomainName)
                       throws java.io.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:
    
    java.io.IOException - if the server cannot be reached
  - getPDPDomainNamesForPDB
```
public java.util.SortedSet<java.lang.String> getPDPDomainNamesForPDB(java.lang.String pdbId)
                                                              throws java.io.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:
    
    java.io.IOException - if the server cannot be reached

Class RemotePDPProvider

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_SERVER

Constructor Detail

RemotePDPProvider

RemotePDPProvider

Method Detail

main

getServer

setServer

getDomain

getPDPDomain

getPDPDomainNamesForPDB