Package org.biojavax

Interface CrossReferenceResolver

All Known Implementing Classes:
BioSQLCrossReferenceResolver, DummyCrossReferenceResolver
public interface CrossReferenceResolver
This interface returns symbols or sequence for a given cross-reference.
Since:
1.5
Author:
Richard Holland, Mark Schreiber

  • Method Details

    • getRemoteSymbolList

      SymbolList getRemoteSymbolList(CrossRef cr, Alphabet a)
      Given a cross reference, return the corresponding symbol list.
      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

      BioEntry getRemoteBioEntry(CrossRef cr) throws CrossReferenceResolutionException
      Given the CrossRef return the corresponding BioEntry
      Parameters:
      cr - the cross reference
      Returns:
      The cross referenced entry (most likely a RichSequence or null if it cannot be found.
      Throws:
      CrossReferenceResolutionException - if a problem occurs during resolution.