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

Class CompositeSequenceParser

java.lang.Object

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

ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser

All Implemented Interfaces:

LineParser<CompositeSequence>, Parser<CompositeSequence>

public class CompositeSequenceParser
extends BasicLineParser<CompositeSequence>

Parse the "old" array description format. This has three columns, with probe id, a genbank id, and a description. Note that this does not set the ArrayDesign for the CompositeSequences, this must be set by the caller.

Author:

pavlidis

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
CompositeSequenceParser()

Method Summary

Modifier and Type	Method	Description
protected void	addResult(CompositeSequence obj)
Collection<CompositeSequence>	getResults()
CompositeSequence	parseOneLine(String line)	Handle the parsing of a single line from the input.

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

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

CompositeSequenceParser

public CompositeSequenceParser()

Method Details

getResults

public Collection<CompositeSequence> getResults()

Specified by:

getResults in interface Parser<CompositeSequence>

Specified by:

getResults in class BasicLineParser<CompositeSequence>

Returns:

the results of the parse.

addResult

protected void addResult(CompositeSequence obj)

Specified by:

addResult in class BasicLineParser<CompositeSequence>

parseOneLine

public CompositeSequence parseOneLine(String line)

Description copied from interface: LineParser

Handle the parsing of a single line from the input.

Parameters:

line - line to parse

Returns:

parsed object