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

Class NcbiGene2AccessionParser

java.lang.Object

ubic.gemma.core.loader.util.parser.BasicLineParser<NCBIGene2Accession>

ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser

All Implemented Interfaces:

LineParser<NCBIGene2Accession>, Parser<NCBIGene2Accession>, QueuingParser<NcbiGeneData>

public class NcbiGene2AccessionParser
extends BasicLineParser<NCBIGene2Accession>
implements QueuingParser<NcbiGeneData>

Class to parse the NCBI gene2accession files. Results are stored in a "Source domain object", not a Gemma Gene.

Author:

pavlidis

See Also:

NCBIGene2Accession

Field Summary

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

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
NcbiGene2AccessionParser()

Method Summary

Modifier and Type	Method	Description
protected void	addResult(NCBIGene2Accession obj)
int	getCount()
Collection<NCBIGene2Accession>	getResults()
void	parse(File f, BlockingQueue<NcbiGeneData> queue1, Map<String,NCBIGeneInfo> geneInfo1)
void	parse(InputStream is)	Parse a InputStream.
void	parse(InputStream is, BlockingQueue<NcbiGeneData> aQueue)	Parse an input stream, storing the results in the passed queue (which can be used by a consumer)
NCBIGene2Accession	parseOneLine(String line)	Handle the parsing of a single line from the input.
void	setStartingNbiId(Integer startingNcbiId)

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

parse, parse

Methods inherited from class java.lang.Object

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

Constructor Detail

NcbiGene2AccessionParser

public NcbiGene2AccessionParser()

Method Detail

parse

public void parse(InputStream is,
                  BlockingQueue<NcbiGeneData> aQueue)
           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<NcbiGeneData>

Parameters:

is - input stream

aQueue - queue

Throws:

IOException - IO problems

parse

public void parse(File f,
                  BlockingQueue<NcbiGeneData> queue1,
                  Map<String,NCBIGeneInfo> geneInfo1)
           throws IOException

Throws:

IOException

parseOneLine

public NCBIGene2Accession parseOneLine(String line)

Description copied from interface: LineParser

Handle the parsing of a single line from the input.

Specified by:

parseOneLine in interface LineParser<NCBIGene2Accession>

Parameters:

line - line to parse

Returns:

parsed object

getResults

public Collection<NCBIGene2Accession> getResults()

Specified by:

getResults in interface Parser<NCBIGene2Accession>

Specified by:

getResults in class BasicLineParser<NCBIGene2Accession>

Returns:

the results of the parse.

parse

public void parse(InputStream is)
           throws IOException

Description copied from interface: Parser

Parse a InputStream.

Specified by:

parse in interface Parser<NCBIGene2Accession>

Overrides:

parse in class BasicLineParser<NCBIGene2Accession>

Parameters:

is - input stream

Throws:

IOException - if there is a problem while manipulating the file

addResult

protected void addResult(NCBIGene2Accession obj)

Specified by:

addResult in class BasicLineParser<NCBIGene2Accession>

getCount

public int getCount()

setStartingNbiId

public void setStartingNbiId(Integer startingNcbiId)