java.lang.Object

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

org.biojava.nbio.structure.scop.CachedRemoteScopInstallation

All Implemented Interfaces:: ScopDatabase

public class CachedRemoteScopInstallation extends SerializableCache<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

Description

CachedRemoteScopInstallation()

CachedRemoteScopInstallation(boolean useCache)
Method Summary

Modifier and Type

Method

Description

List<ScopDescription>

filterByClassificationId(String query)

Get all scop descriptions that start with a classification ID, e.g.

List<ScopDescription>

filterByDescription(String query)

Get all scop descriptions that start with a certain name.

List<ScopDomain>

filterByDomainName(String query)

search through SCOP and filter based on domain name

void

flushCache()

List<ScopDescription>

getByCategory(ScopCategory category)

Get all records of a particular classification.

List<String>

getComments(int sunid)

Get comments about a SCOP domain by its sunid

ScopDomain

getDomainByScopID(String scopId)

get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)

List<ScopDomain>

getDomainsForPDB(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.

List<ScopDomain>

getScopDomainsBySunid(Integer sunid)

Get a SCOP domain by its sunid

ScopNode

getScopNode(int sunid)

Access a particular ScopNode.

String

getScopVersion()

Returns the SCOP version

List<ScopNode>

getTree(ScopDomain domain)

get the SCOP sub-tree for a particular domain.

void

setScopVersion(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 Details
- CachedRemoteScopInstallation
  
  public CachedRemoteScopInstallation() throws IOException
  
  Throws:
  
  IOException
- CachedRemoteScopInstallation
  
  public CachedRemoteScopInstallation(boolean useCache) throws IOException
  
  Throws:
  
  IOException
Method Details
- getByCategory
  
  public 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 List<ScopDescription> filterByClassificationId(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 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 List<ScopDomain> filterByDomainName(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 List<ScopDescription> filterByDescription(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 List<ScopDomain> getDomainsForPDB(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(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 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(String version)
  
  Description copied from interface: ScopDatabase
  
  Sets the scop version used.
  
  Specified by:
  
  setScopVersion in interface ScopDatabase
- getScopDomainsBySunid
  
  public List<ScopDomain> getScopDomainsBySunid(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<String,ScopDomain>
- getComments
  
  public List<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 Details

CachedRemoteScopInstallation

CachedRemoteScopInstallation

Method Details

getByCategory

filterByClassificationId

getTree

filterByDomainName

filterByDescription

getScopDescriptionBySunid

getDomainsForPDB

getDomainByScopID

getScopNode

getScopVersion

setScopVersion

getScopDomainsBySunid

flushCache

getComments