Package ubic.gemma.core.loader.genome.taxon

Class TaxonParser

java.lang.Object

ubic.gemma.core.loader.util.parser.BasicLineMapParser<Integer,Taxon>

ubic.gemma.core.loader.genome.taxon.TaxonParser

All Implemented Interfaces:

LineParser<Taxon>, Parser<Taxon>

public class TaxonParser
extends BasicLineMapParser<Integer,Taxon>

Parse the "names.dmp" file from NCBI, ftp://ftp.ncbi.nih.gov/pub/taxonomy/.

Author:

pavlidis

Field Summary

Fields inherited from class ubic.gemma.core.loader.util.parser.BasicLineMapParser

COMMENT_MARK, log

Fields inherited from interface ubic.gemma.core.loader.util.parser.LineParser

MIN_PARSED_LINES_FOR_UPDATE, PARSE_ALERT_TIME_FREQUENCY_MS

Fields inherited from interface ubic.gemma.core.loader.util.parser.Parser

PARSE_ALERT_FREQUENCY

Constructor Summary

Constructors

Constructor	Description
TaxonParser()

Method Summary

Modifier and Type	Method	Description
boolean	containsKey(Integer key)
Taxon	get(Integer key)
protected Integer	getKey(Taxon newItem)
Collection<Integer>	getKeySet()
Collection<Taxon>	getResults()
Taxon	parseOneLine(String line)	Handle the parsing of a single line from the input.
protected void	put(Integer key, Taxon value)

Methods inherited from class ubic.gemma.core.loader.util.parser.BasicLineMapParser

parse, parse, parse

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.loader.util.parser.Parser

getUniqueResult

Constructor Details

TaxonParser

public TaxonParser()

Method Details

containsKey

public boolean containsKey(Integer key)

Specified by:

containsKey in class BasicLineMapParser<Integer,Taxon>

get

public Taxon get(Integer key)

Specified by:

get in class BasicLineMapParser<Integer,Taxon>

getKeySet

public Collection<Integer> getKeySet()

Specified by:

getKeySet in class BasicLineMapParser<Integer,Taxon>

getResults

public Collection<Taxon> getResults()

Specified by:

getResults in interface Parser<Taxon>

Specified by:

getResults in class BasicLineMapParser<Integer,Taxon>

Returns:

the results of the parse.

parseOneLine

public Taxon parseOneLine(String line)

Description copied from interface: LineParser

Handle the parsing of a single line from the input.

Specified by:

parseOneLine in interface LineParser<Taxon>

Specified by:

parseOneLine in class BasicLineMapParser<Integer,Taxon>

Parameters:

line - line to parse

Returns:

parsed object

getKey

protected Integer getKey(Taxon newItem)

Specified by:

getKey in class BasicLineMapParser<Integer,Taxon>

put

protected void put(Integer key,
 Taxon value)

Specified by:

put in class BasicLineMapParser<Integer,Taxon>