Package ubic.gemma.core.loader.expression.arrayDesign

Class AffyProbeReader

java.lang.Object

ubic.gemma.core.loader.util.parser.BasicLineMapParser<CompositeSequence,Collection<Reporter>>

ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader

All Implemented Interfaces:

LineParser<Collection<Reporter>>, Parser<Collection<Reporter>>

public class AffyProbeReader
extends BasicLineMapParser<CompositeSequence,Collection<Reporter>>

Reads Affymetrix Probe files, including exon arrays.

Expected format is tabbed, NOT FASTA. A one-line header starting with the word "Probe" is REQUIRED. In later versions of the format the second field of the file (column) is omitted.

For 3' arrays, here is an example:

 1494_f_at 1 325 359 1118 TCCCCATGAGTTTGGCCCGCAGAGT Antisense
 

For exon arrays, we create the equivalent files from the GFF files provided by Affymetrix. The files are created off-line using a PERL script.

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
AffyProbeReader()

Method Summary

Modifier and Type	Method	Description
boolean	containsKey(CompositeSequence key)
Collection<Reporter>	get(CompositeSequence key)
protected CompositeSequence	getKey(Collection<Reporter> newItem)
Collection<CompositeSequence>	getKeySet()
Collection<Collection<Reporter>>	getResults()
void	parse(InputStream is)	Parse a InputStream.
Collection<Reporter>	parseOneLine(String line)	Handle the parsing of a single line from the input.
protected void	put(CompositeSequence key, Collection<Reporter> value)
void	setSequenceField(int sequenceField)	Set the index (starting from zero) of the field where the sequence is found.

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

parse, parse

Methods inherited from class java.lang.Object

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

Constructor Detail

AffyProbeReader

public AffyProbeReader()

Method Detail

setSequenceField

public void setSequenceField(int sequenceField)

Set the index (starting from zero) of the field where the sequence is found. This varies in the Affymetrix-provided files.

Parameters:

sequenceField - sequence field

containsKey

public boolean containsKey(CompositeSequence key)

Specified by:

containsKey in class BasicLineMapParser<CompositeSequence,Collection<Reporter>>

get

public Collection<Reporter> get(CompositeSequence key)

Specified by:

get in class BasicLineMapParser<CompositeSequence,Collection<Reporter>>

getKeySet

public Collection<CompositeSequence> getKeySet()

Specified by:

getKeySet in class BasicLineMapParser<CompositeSequence,Collection<Reporter>>

getResults

public Collection<Collection<Reporter>> getResults()

Specified by:

getResults in interface Parser<Collection<Reporter>>

Specified by:

getResults in class BasicLineMapParser<CompositeSequence,Collection<Reporter>>

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<Collection<Reporter>>

Overrides:

parse in class BasicLineMapParser<CompositeSequence,Collection<Reporter>>

Parameters:

is - input stream

Throws:

IOException - if there is a problem while manipulating the file

parseOneLine

public Collection<Reporter> parseOneLine(String line)

Description copied from interface: LineParser

Handle the parsing of a single line from the input.

Specified by:

parseOneLine in interface LineParser<Collection<Reporter>>

Specified by:

parseOneLine in class BasicLineMapParser<CompositeSequence,Collection<Reporter>>

Parameters:

line - line to parse

Returns:

parsed object

getKey

protected CompositeSequence getKey(Collection<Reporter> newItem)

Specified by:

getKey in class BasicLineMapParser<CompositeSequence,Collection<Reporter>>

put

protected void put(CompositeSequence key,
                   Collection<Reporter> value)

Specified by:

put in class BasicLineMapParser<CompositeSequence,Collection<Reporter>>