Package ubic.gemma.core.loader.genome.gene.ncbi

Class NcbiGeneHistoryParser

java.lang.Object

ubic.gemma.core.loader.util.parser.BasicLineMapParser<String,NcbiGeneHistory>

ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser

All Implemented Interfaces:

LineParser<NcbiGeneHistory>, Parser<NcbiGeneHistory>

public class NcbiGeneHistoryParser
extends BasicLineMapParser<String,NcbiGeneHistory>

Parse the NCBI "gene_history" file. File format : tax_id, GeneID,Discontinued_GeneID, Discontinued_Symbol, Discontinue_Date; (tab is used as a separator, pound sign - start of a comment) File is obtained from ftp.ncbi.nih.gov.gene/DATA See ncbi readme There are two kinds of lines. Lines with a "-" for the GeneID (the majority) seems to be used when the record was withdrawn (Field is defined as "the current unique identified for a gene"). Lines with a symbol means it was replaced, so far as I can tell.

Author:

paul

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
NcbiGeneHistoryParser()

Method Summary

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

Constructor Detail

NcbiGeneHistoryParser

public NcbiGeneHistoryParser()

Method Detail

containsKey

public boolean containsKey(String key)

Specified by:

containsKey in class BasicLineMapParser<String,NcbiGeneHistory>

get

public NcbiGeneHistory get(String key)

Specified by:

get in class BasicLineMapParser<String,NcbiGeneHistory>

getKeySet

public Collection<String> getKeySet()

Specified by:

getKeySet in class BasicLineMapParser<String,NcbiGeneHistory>

getResults

public Collection<NcbiGeneHistory> getResults()

Specified by:

getResults in interface Parser<NcbiGeneHistory>

Specified by:

getResults in class BasicLineMapParser<String,NcbiGeneHistory>

Returns:

the results of the parse.

parseOneLine

public NcbiGeneHistory parseOneLine(String line)

Description copied from interface: LineParser

Handle the parsing of a single line from the input.

Specified by:

parseOneLine in interface LineParser<NcbiGeneHistory>

Specified by:

parseOneLine in class BasicLineMapParser<String,NcbiGeneHistory>

Parameters:

line - line to parse

Returns:

parsed object

getKey

protected String getKey(NcbiGeneHistory newItem)

Specified by:

getKey in class BasicLineMapParser<String,NcbiGeneHistory>

put

protected void put(String key,
                   NcbiGeneHistory value)

Specified by:

put in class BasicLineMapParser<String,NcbiGeneHistory>

discontinuedIdForSymbol

public String discontinuedIdForSymbol(String geneSymbol,
                                      Integer taxonId)

Parameters:

geneSymbol - gene symbol

taxonId - taxon id

Returns:

null, or the NCBI ID of the gene that was discontinued.