Package ubic.gemma.core.loader.expression.geo

Class GeoFamilyParser

java.lang.Object

ubic.gemma.core.loader.expression.geo.GeoFamilyParser

All Implemented Interfaces:

Parser<GeoParseResult>

public class GeoFamilyParser
extends Object
implements Parser<GeoParseResult>

Class for parsing GSE and GDS files from NCBI GEO. See ncbi geo for format information.

Author:

keshav, pavlidis

Field Summary

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

PARSE_ALERT_FREQUENCY

Constructor Summary

Constructors

Constructor	Description
GeoFamilyParser()

Method Summary

Modifier and Type	Method	Description
static GeoSeriesType	convertStringToSeriesType(String string)	See also GeoDataset.convertStringToExperimentType
Collection<GeoParseResult>	getResults()
void	parse(File f)	Parse a File
void	parse(InputStream is)	Parse a InputStream.
void	parse(String fileName)	Parse a file identified by its path.
void	sampleTypeSet(String accession, String string)
void	setProcessPlatformsOnly(boolean b)

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 Detail

GeoFamilyParser

public GeoFamilyParser()

Method Detail

getResults

public Collection<GeoParseResult> getResults()

Specified by:

getResults in interface Parser<GeoParseResult>

Returns:

the results of the parse.

parse

public void parse(File f)
           throws IOException

Description copied from interface: Parser

Parse a File

Specified by:

parse in interface Parser<GeoParseResult>

Parameters:

f - file

Throws:

IOException - if there is a problem while manipulating the file

parse

public void parse(InputStream is)
           throws IOException

Description copied from interface: Parser

Parse a InputStream.

Specified by:

parse in interface Parser<GeoParseResult>

Parameters:

is - input stream

Throws:

IOException - if there is a problem while manipulating the file

parse

public void parse(String fileName)
           throws IOException

Description copied from interface: Parser

Parse a file identified by its path.

Specified by:

parse in interface Parser<GeoParseResult>

Parameters:

fileName - Absolute path to the file

Throws:

IOException - if there is a problem while manipulating the file

sampleTypeSet

public void sampleTypeSet(String accession,
                          String string)

setProcessPlatformsOnly

public void setProcessPlatformsOnly(boolean b)

convertStringToSeriesType

public static GeoSeriesType convertStringToSeriesType(String string)

See also GeoDataset.convertStringToExperimentType

Parameters:

string - series type string

Returns:

series type object