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

Class NcbiGeneInfoParser

java.lang.Object

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

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

All Implemented Interfaces:

LineParser<NCBIGeneInfo>, Parser<NCBIGeneInfo>, QueuingParser<String>

public class NcbiGeneInfoParser
extends BasicLineMapParser<String,NCBIGeneInfo>
implements QueuingParser<String>

Class to parse the gene_info file from NCBI Gene. See readme for details of the format.

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
NcbiGeneInfoParser()

Method Summary

Modifier and Type	Method	Description
boolean	containsKey(String key)
NCBIGeneInfo	get(String key)
String	getKey(NCBIGeneInfo newItem)
Collection<String>	getKeySet()
Collection<NCBIGeneInfo>	getResults()
void	parse(InputStream inputStream, BlockingQueue<String> queue)	Parse an input stream, storing the results in the passed queue (which can be used by a consumer)
NCBIGeneInfo	parseOneLine(String line)	Handle the parsing of a single line from the input.
protected void	put(String key, NCBIGeneInfo value)
void	setFilter(boolean filter)
void	setSupportedTaxa(Collection<Integer> ncbiTaxonIds)

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

NcbiGeneInfoParser

public NcbiGeneInfoParser()

Method Details

containsKey

public boolean containsKey(String key)

Specified by:

containsKey in class BasicLineMapParser<String,NCBIGeneInfo>

get

public NCBIGeneInfo get(String key)

Specified by:

get in class BasicLineMapParser<String,NCBIGeneInfo>

getKeySet

public Collection<String> getKeySet()

Specified by:

getKeySet in class BasicLineMapParser<String,NCBIGeneInfo>

getResults

public Collection<NCBIGeneInfo> getResults()

Specified by:

getResults in interface Parser<NCBIGeneInfo>

Specified by:

getResults in class BasicLineMapParser<String,NCBIGeneInfo>

Returns:

the results of the parse.

parseOneLine

public NCBIGeneInfo parseOneLine(String line)

Description copied from interface: LineParser

Handle the parsing of a single line from the input.

Specified by:

parseOneLine in interface LineParser<NCBIGeneInfo>

Specified by:

parseOneLine in class BasicLineMapParser<String,NCBIGeneInfo>

Parameters:

line - line to parse

Returns:

parsed object

getKey

public String getKey(NCBIGeneInfo newItem)

Specified by:

getKey in class BasicLineMapParser<String,NCBIGeneInfo>

put

protected void put(String key,
 NCBIGeneInfo value)

Specified by:

put in class BasicLineMapParser<String,NCBIGeneInfo>

parse

public void parse(InputStream inputStream,
 BlockingQueue<String> queue)
           throws IOException

Description copied from interface: QueuingParser

Parse an input stream, storing the results in the passed queue (which can be used by a consumer)

Specified by:

parse in interface QueuingParser<String>

Parameters:

inputStream - input stream

queue - queue

Throws:

IOException - IO problems

setFilter

public void setFilter(boolean filter)

setSupportedTaxa

public void setSupportedTaxa(Collection<Integer> ncbiTaxonIds)

Parameters:

ncbiTaxonIds - Taxon IDs (NCBI, not Gemma ids) e.g. 9606 for H. sapiens