Package org.biojavax.bio.db.biosql
Class BioSQLCrossReferenceResolver
java.lang.Object
org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver
- All Implemented Interfaces:
CrossReferenceResolver
A simple implementation of CrossReferenceResolver
- Since:
- 1.5
- Author:
- Richard Holland, Mark Schreiber, David Scott
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Constructor Summary
ConstructorsConstructorDescriptionBioSQLCrossReferenceResolver
(Object session) Requires a Hibernate session to work correctly. -
Method Summary
Modifier and TypeMethodDescriptionGiven theCrossRef
return the correspondingBioEntry
getRemoteSymbolList
(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list.
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Constructor Details
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BioSQLCrossReferenceResolver
Requires a Hibernate session to work correctly. The session parameter is a Hibernate Session object and must not be null. It is this session that database objects will be retrieved from/persisted to.- See Also:
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Method Details
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getRemoteSymbolList
Given a cross reference, return the corresponding symbol list.- Specified by:
getRemoteSymbolList
in interfaceCrossReferenceResolver
- Parameters:
cr
- the cross reference to look up.a
- the alphabet to construct the infinitely ambiguous symbol list over if it cannot be found.- Returns:
- the symbol list matching it. If none, return an infintely-ambiguous symbol list rather than null.
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getRemoteBioEntry
Given theCrossRef
return the correspondingBioEntry
- Specified by:
getRemoteBioEntry
in interfaceCrossReferenceResolver
- Parameters:
cr
- the cross reference- Returns:
- The cross referenced entry (most likely a
RichSequence
or null if it cannot be found.
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