Package org.biojava.nbio.structure.scop
Interface ScopDatabase
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- All Known Subinterfaces:
LocalScopDatabase
- All Known Implementing Classes:
BerkeleyScopInstallation
,CachedRemoteScopInstallation
,RemoteScopInstallation
,ScopInstallation
public interface ScopDatabase
General API how to interact with SCOP- Since:
- 3.0.2
- Author:
- Andreas Prlic
- See Also:
LocalScopDatabase
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method 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 namejava.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 sunidScopDomain
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 IDScopDescription
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 sunidScopNode
getScopNode(int sunid)
Access a particular ScopNode.java.lang.String
getScopVersion()
Returns the SCOP versionjava.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.
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Method Detail
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getByCategory
java.util.List<ScopDescription> getByCategory(ScopCategory category)
Get all records of a particular classification.- Parameters:
category
- e.g. "superfamily"- Returns:
- all records of this type
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filterByClassificationId
java.util.List<ScopDescription> filterByClassificationId(java.lang.String query)
Get all scop descriptions that start with a classification ID, e.g. b.1.18- Parameters:
query
-- Returns:
- list of scop descriptions
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getTree
java.util.List<ScopNode> getTree(ScopDomain domain)
get the SCOP sub-tree for a particular domain.- Parameters:
domain
-- Returns:
- list of ScopNodes providing the path to this domain
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filterByDomainName
java.util.List<ScopDomain> filterByDomainName(java.lang.String query)
search through SCOP and filter based on domain name- Parameters:
query
- a (part) of a name- Returns:
- list of matchin ScopDomains
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filterByDescription
java.util.List<ScopDescription> filterByDescription(java.lang.String query)
Get all scop descriptions that start with a certain name. e.g. Globin- Parameters:
query
-- Returns:
- list of scop descriptions
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getScopDescriptionBySunid
ScopDescription getScopDescriptionBySunid(int sunid)
Return the SCOP description for a node in the hierarchy by its "sunid" id.- Parameters:
sunid
-- Returns:
- a ScopDescription object
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getDomainsForPDB
java.util.List<ScopDomain> getDomainsForPDB(java.lang.String pdbId)
Get a list of ScopDomains that have been assigned to a PDB ID- Parameters:
pdbId
- the PDB entry- Returns:
- a list of ScopDomains
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getDomainByScopID
ScopDomain getDomainByScopID(java.lang.String scopId)
get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)- Parameters:
scopId
- e.g. d2bq6a1- Returns:
- a ScopDomain or null if no domain with the particular ID could be found
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getScopNode
ScopNode getScopNode(int sunid)
Access a particular ScopNode. The scopNode then allows to traverse through the scop hierarchy...- Parameters:
sunid
- the scop unique id- Returns:
- a ScopNode that matches this sunid
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getScopVersion
java.lang.String getScopVersion()
Returns the SCOP version- Returns:
- version of SCOP
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setScopVersion
void setScopVersion(java.lang.String version)
Sets the scop version used.- Parameters:
version
-- Throws:
java.lang.UnsupportedOperationException
- If the version cannot be changed
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getScopDomainsBySunid
java.util.List<ScopDomain> getScopDomainsBySunid(java.lang.Integer sunid)
Get a SCOP domain by its sunid- Parameters:
sunid
- the scop unique id- Returns:
- a list of scop domains that match this sunid
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getComments
java.util.List<java.lang.String> getComments(int sunid)
Get comments about a SCOP domain by its sunid- Parameters:
sunid
-- Returns:
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