org.biojavax

Class DummyCrossReferenceResolver

java.lang.Object

org.biojavax.DummyCrossReferenceResolver

All Implemented Interfaces:

CrossReferenceResolver

public class DummyCrossReferenceResolver
extends Object
implements CrossReferenceResolver

A simple implementation of CrossReferenceResolver.

Since:

1.5

Author:

Richard Holland, Mark Schreiber

Constructor Summary

Constructors

Constructor and Description
DummyCrossReferenceResolver()

Method Summary

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.

Methods inherited from class java.lang.Object

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

Constructor Detail

DummyCrossReferenceResolver

public DummyCrossReferenceResolver()

Method Detail

getRemoteSymbolList

public SymbolList getRemoteSymbolList(CrossRef cr,
                                      Alphabet a)

Given a cross reference, return the corresponding symbol list. All responses are instances of InfinitelyAmbiguousSymbolList.

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 All responses are null.

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.