CachedRemoteScopInstallation

java.lang.Object
- org.biojava.nbio.structure.domain.SerializableCache<java.lang.String,ScopDomain>
- - org.biojava.nbio.structure.scop.CachedRemoteScopInstallation

All Implemented Interfaces:

ScopDatabase
```
public class CachedRemoteScopInstallation
extends SerializableCache<java.lang.String,ScopDomain>
implements ScopDatabase
```
An extension of the RemoteScopInstallation that caches some of the data locally.

Author:

Andreas Prlic

Field Summary
- Fields inherited from class org.biojava.nbio.structure.domain.SerializableCache
  cacheFileName, serializedCache

Constructor Summary

Constructors
Constructor and Description

CachedRemoteScopInstallation()

CachedRemoteScopInstallation(boolean useCache)

Constructors
Constructor and Description
`CachedRemoteScopInstallation()`
`CachedRemoteScopInstallation(boolean useCache)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.util.List<ScopDescription>`	`filterByClassificationId(java.lang.String query)` Get all scop descriptions that start with a classification ID, e.g.
`java.util.List<ScopDescription>`	`filterByDescription(java.lang.String query)` Get all scop descriptions that start with a certain name.
`java.util.List<ScopDomain>`	`filterByDomainName(java.lang.String query)` search through SCOP and filter based on domain name
`void`	`flushCache()`
`java.util.List<ScopDescription>`	`getByCategory(ScopCategory category)` Get all records of a particular classification.
`java.util.List<java.lang.String>`	`getComments(int sunid)` Get comments about a SCOP domain by its sunid
`ScopDomain`	`getDomainByScopID(java.lang.String scopId)` get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
`java.util.List<ScopDomain>`	`getDomainsForPDB(java.lang.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.
`java.util.List<ScopDomain>`	`getScopDomainsBySunid(java.lang.Integer sunid)` Get a SCOP domain by its sunid
`ScopNode`	`getScopNode(int sunid)` Access a particular ScopNode.
`java.lang.String`	`getScopVersion()` Returns the SCOP version
`java.util.List<ScopNode>`	`getTree(ScopDomain domain)` get the SCOP sub-tree for a particular domain.
`void`	`setScopVersion(java.lang.String version)` Sets the scop version used.

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

- Constructor Detail
  - CachedRemoteScopInstallation
```
public CachedRemoteScopInstallation()
                             throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - CachedRemoteScopInstallation
```
public CachedRemoteScopInstallation(boolean useCache)
                             throws java.io.IOException
```
    Throws:
    
    java.io.IOException
- Method Detail
  - getByCategory
```
public java.util.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 java.util.List<ScopDescription> filterByClassificationId(java.lang.String query)
```
    Description copied from interface: ScopDatabase
    
    Get all scop descriptions that start with a classification ID, e.g. b.1.18
    
    Specified by:
    
    filterByClassificationId in interface ScopDatabase
    
    Returns:
    
    list of scop descriptions
  - getTree
```
public java.util.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 java.util.List<ScopDomain> filterByDomainName(java.lang.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 java.util.List<ScopDescription> filterByDescription(java.lang.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 java.util.List<ScopDomain> getDomainsForPDB(java.lang.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(java.lang.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 java.lang.String getScopVersion()
```
    Description copied from interface: ScopDatabase
    
    Returns the SCOP version
    
    Specified by:
    
    getScopVersion in interface ScopDatabase
    
    Returns:
    
    version of SCOP
  - setScopVersion
```
public void setScopVersion(java.lang.String version)
```
    Description copied from interface: ScopDatabase
    
    Sets the scop version used.
    
    Specified by:
    
    setScopVersion in interface ScopDatabase
  - getScopDomainsBySunid
```
public java.util.List<ScopDomain> getScopDomainsBySunid(java.lang.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
  - flushCache
```
public void flushCache()
```
    Overrides:
    
    flushCache in class SerializableCache<java.lang.String,ScopDomain>
  - getComments
```
public java.util.List<java.lang.String> getComments(int sunid)
```
    Description copied from interface: ScopDatabase
    
    Get comments about a SCOP domain by its sunid
    
    Specified by:
    
    getComments in interface ScopDatabase
    
    Returns:

Class CachedRemoteScopInstallation

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

Constructor Detail

CachedRemoteScopInstallation

CachedRemoteScopInstallation

Method Detail

getByCategory

filterByClassificationId

getTree

filterByDomainName

filterByDescription

getScopDescriptionBySunid

getDomainsForPDB

getDomainByScopID

getScopNode

getScopVersion

setScopVersion

getScopDomainsBySunid

flushCache

getComments