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 Summary

Methods

Modifier and Type	Method and 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.

Method Detail

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.