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 Details

    • 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:

  • Method Details

    • 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.