com.hfg.bio.taxonomy.ncbi

Class NCBITaxonomyDataSourceImpl

java.lang.Object

com.hfg.bio.taxonomy.ncbi.NCBITaxonomyDataSourceImpl

All Implemented Interfaces:

NCBITaxonomyDataSource

Direct Known Subclasses:

NCBIRemoteTaxonomyDataSource

public abstract class NCBITaxonomyDataSourceImpl
extends Object
implements NCBITaxonomyDataSource

Base class for implementing an NCBI taxonomy data source.

Field Summary

Fields

Modifier and Type	Field and Description
protected static Pattern	sSnCnPattern

Constructor Summary

Constructors

Constructor and Description
NCBITaxonomyDataSourceImpl()

Method Summary

Modifier and Type	Method and Description
protected void	addToNameMap(String inName, NCBITaxon inTaxon)
Set<NCBITaxon>	getByName(String inValue) Retrieves the NCBITaxon for the specified common name, scientific name, or GenBank common name.
NCBITaxon	getByTaxonId(int inValue) Retrieves the taxon for the specified NCBI taxon id.
protected abstract void	initialize()
protected void	innerParseNamesFile(BufferedReader inReader)
protected void	innerParseNodesFile(BufferedReader inReader)

Methods inherited from class java.lang.Object

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

Field Detail

sSnCnPattern

protected static final Pattern sSnCnPattern

Constructor Detail

NCBITaxonomyDataSourceImpl

public NCBITaxonomyDataSourceImpl()

Method Detail

initialize

protected abstract void initialize()

getByTaxonId

public NCBITaxon getByTaxonId(int inValue)

Description copied from interface: NCBITaxonomyDataSource

Retrieves the taxon for the specified NCBI taxon id.

Specified by:

getByTaxonId in interface NCBITaxonomyDataSource

Parameters:

inValue - the taxon id for the taxon object to retrieve

Returns:

the taxon object corresponding to the specified id. Returns null if the taxon cannot be found.

getByName

public Set<NCBITaxon> getByName(String inValue)

Description copied from interface: NCBITaxonomyDataSource

Retrieves the NCBITaxon for the specified common name, scientific name, or GenBank common name. Generally there will be a single taxon found for a given name, but there are instances where multiple taxons may be found.

Specified by:

getByName in interface NCBITaxonomyDataSource

Parameters:

inValue - the species name (common or scientific) for the taxon object to return

Returns:

a Set of taxon objects corresponding to the specified name. Returns null if a match cannot be found.

innerParseNodesFile

protected void innerParseNodesFile(BufferedReader inReader)
                            throws IOException

Throws:

IOException

innerParseNamesFile

protected void innerParseNamesFile(BufferedReader inReader)
                            throws IOException

Throws:

IOException

addToNameMap

protected void addToNameMap(String inName,
                            NCBITaxon inTaxon)