uk.ac.ebi.intact.util
Class BioSourceFactory

java.lang.Object
  |
  +--uk.ac.ebi.intact.util.BioSourceFactory

public class BioSourceFactory

extends java.lang.Object

That class his hidding the logic which allow to get a valid biosource from a taxid.

Version:

$Id: BioSourceFactory.java,v 1.5 2004/03/24 15:15:11 skerrien Exp $

Author:

Samuel Kerrien (skerrien@ebi.ac.uk)

Constructor Summary

BioSourceFactory(IntactHelper helper)

BioSourceFactory(IntactHelper helper, Institution institution)

BioSourceFactory(IntactHelper helper, Institution institution, int cacheSize)

Method Summary

java.lang.String	getUpToDateTaxid(java.lang.String taxid) Gives a valid taxid.
BioSource	getValidBioSource(java.lang.String aTaxId) Create or update a BioSource object from a taxid.
void	setLogger(org.apache.log4j.Logger logger) Set a logger to keep track of the internal processing.

Methods inherited from class java.lang.Object

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

Constructor Detail

BioSourceFactory

public BioSourceFactory(IntactHelper helper)
                 throws IntactException

BioSourceFactory

public BioSourceFactory(IntactHelper helper,
                        Institution institution)

BioSourceFactory

public BioSourceFactory(IntactHelper helper,
                        Institution institution,
                        int cacheSize)

Method Detail

setLogger

public void setLogger(org.apache.log4j.Logger logger)

Set a logger to keep track of the internal processing.

Parameters:

logger - the logger to set

getValidBioSource

public BioSource getValidBioSource(java.lang.String aTaxId)
                            throws IntactException

Create or update a BioSource object from a taxid.

Parameters:

aTaxId - The tax id to create/update a biosource for

Returns:

a valid, persistent BioSource

IntactException

getUpToDateTaxid

public java.lang.String getUpToDateTaxid(java.lang.String taxid)
                                  throws IntactException

Gives a valid taxid.

Parameters:

taxid - the original taxid

Returns:

a valid taxid (can be different from the original in case of obsoletness).

Throws:

IntactException - if an error occur when accessing IntAct or an inconstistancy.