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

Class IlluminaProbeReader

java.lang.Object

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

ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader

All Implemented Interfaces:

LineParser<Reporter>, Parser<Reporter>

public class IlluminaProbeReader
extends BasicLineMapParser<String,Reporter>

Parse an Illumina "manifest.txt" file (tab-delimited). A one-line header is permitted.

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
IlluminaProbeReader()

Method Summary

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

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

getUniqueResult

Constructor Details

IlluminaProbeReader

public IlluminaProbeReader()

Method Details

containsKey

public boolean containsKey(String key)

Specified by:

containsKey in class BasicLineMapParser<String,Reporter>

get

public Reporter get(String key)

Specified by:

get in class BasicLineMapParser<String,Reporter>

getKeySet

public Collection<String> getKeySet()

Specified by:

getKeySet in class BasicLineMapParser<String,Reporter>

getResults

public Collection<Reporter> getResults()

Specified by:

getResults in interface Parser<Reporter>

Specified by:

getResults in class BasicLineMapParser<String,Reporter>

Returns:

the results of the parse.

parseOneLine

public 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<Reporter>

Specified by:

parseOneLine in class BasicLineMapParser<String,Reporter>

Parameters:

line - line to parse

Returns:

parsed object

getKey

protected String getKey(Reporter newItem)

Specified by:

getKey in class BasicLineMapParser<String,Reporter>

put

protected void put(String key,
 Reporter value)

Specified by:

put in class BasicLineMapParser<String,Reporter>