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java.lang.Objectorg.biojava.bio.structure.domain.SerializableCache<String,ScopDomain>
org.biojava.bio.structure.scop.CachedRemoteScopInstallation
public class CachedRemoteScopInstallation
An extension of the RemoteScopInstallation that caches some of the data locally.
Field Summary |
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Fields inherited from class org.biojava.bio.structure.domain.SerializableCache |
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cacheFileName, serializedCache |
Constructor Summary | |
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CachedRemoteScopInstallation()
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CachedRemoteScopInstallation(boolean useCache)
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Method Summary | |
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List<ScopDescription> |
filterByClassificationId(String query)
Get all scop descriptions that start with a classifcation 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()
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List<ScopDescription> |
getByCategory(ScopCategory category)
Get all records of a particular classification. |
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. |
Methods inherited from class org.biojava.bio.structure.domain.SerializableCache |
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cache, disableCache, enableCache, get, isCacheEnabled, isDebug, reloadFromFile, setDebug |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public CachedRemoteScopInstallation()
public CachedRemoteScopInstallation(boolean useCache)
Method Detail |
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public List<ScopDescription> getByCategory(ScopCategory category)
ScopDatabase
getByCategory
in interface ScopDatabase
category
- e.g. "superfamily"
public List<ScopDescription> filterByClassificationId(String query)
ScopDatabase
filterByClassificationId
in interface ScopDatabase
public List<ScopNode> getTree(ScopDomain domain)
ScopDatabase
getTree
in interface ScopDatabase
public List<ScopDomain> filterByDomainName(String query)
ScopDatabase
filterByDomainName
in interface ScopDatabase
query
- a (part) of a name
public List<ScopDescription> filterByDescription(String query)
ScopDatabase
filterByDescription
in interface ScopDatabase
public ScopDescription getScopDescriptionBySunid(int sunid)
ScopDatabase
getScopDescriptionBySunid
in interface ScopDatabase
public List<ScopDomain> getDomainsForPDB(String pdbId)
ScopDatabase
getDomainsForPDB
in interface ScopDatabase
pdbId
- the PDB entry
public ScopDomain getDomainByScopID(String scopId)
ScopDatabase
getDomainByScopID
in interface ScopDatabase
scopId
- e.g. d2bq6a1
public ScopNode getScopNode(int sunid)
ScopDatabase
getScopNode
in interface ScopDatabase
sunid
- the scop unique id
public String getScopVersion()
ScopDatabase
getScopVersion
in interface ScopDatabase
public List<ScopDomain> getScopDomainsBySunid(Integer sunid)
ScopDatabase
getScopDomainsBySunid
in interface ScopDatabase
sunid
- the scop unique id
public void flushCache()
flushCache
in class SerializableCache<String,ScopDomain>
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