Package org.biojavax.bio.db.biosql

Class BioSQLCrossReferenceResolver

java.lang.Object

org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver

All Implemented Interfaces:

CrossReferenceResolver

public class BioSQLCrossReferenceResolver
extends Object
implements CrossReferenceResolver

A simple implementation of CrossReferenceResolver

Since:

1.5

Author:

Richard Holland, Mark Schreiber, David Scott

Constructor Summary

Constructors

Constructor	Description
BioSQLCrossReferenceResolver(Object session)	Requires a Hibernate session to work correctly.

Method Summary

Modifier and Type	Method	Description
BioEntry	getRemoteBioEntry(CrossRef cr)	Given the CrossRef return the corresponding BioEntry
SymbolList	getRemoteSymbolList(CrossRef cr, Alphabet a)	Given a cross reference, return the corresponding symbol list.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BioSQLCrossReferenceResolver

public BioSQLCrossReferenceResolver(Object session)

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:

org.hibernate.Session

Method Detail

getRemoteSymbolList

public SymbolList getRemoteSymbolList(CrossRef cr,
                                      Alphabet a)

Given a cross reference, return the corresponding symbol list.

Specified by:

getRemoteSymbolList in interface CrossReferenceResolver

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.

getRemoteBioEntry

public BioEntry getRemoteBioEntry(CrossRef cr)

Given the CrossRef return the corresponding BioEntry

Specified by:

getRemoteBioEntry in interface CrossReferenceResolver

Parameters:

cr - the cross reference

Returns:

The cross referenced entry (most likely a RichSequence or null if it cannot be found.