Package ubic.gemma.core.loader.genome

Class FastaParser

java.lang.Object

ubic.gemma.core.loader.util.parser.RecordParser<BioSequence>

ubic.gemma.core.loader.genome.FastaParser

All Implemented Interfaces:

Parser<BioSequence>

public class FastaParser
extends RecordParser<BioSequence>

FASTA sequence file parser. Results are in BioSequence objects. Parsing a single record

Author:

pavlidis

Field Summary

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

log

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

PARSE_ALERT_FREQUENCY

Constructor Summary

Constructors

Constructor	Description
FastaParser()

Method Summary

Modifier and Type	Method	Description
protected void	addResult(Object obj)	Add an object to the results collection.
Collection<BioSequence>	getResults()
Object	parseOneRecord(String record)	Handle the parsing of a single record from the input.

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

parse, parse, parse, setRecordSeparator

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaParser

public FastaParser()

Method Detail

getResults

public Collection<BioSequence> getResults()

Specified by:

getResults in interface Parser<BioSequence>

Specified by:

getResults in class RecordParser<BioSequence>

Returns:

the results of the parse.

parseOneRecord

public Object parseOneRecord(String record)

Description copied from class: RecordParser

Handle the parsing of a single record from the input.

Specified by:

parseOneRecord in class RecordParser<BioSequence>

Parameters:

record - record

Returns:

parsed object

addResult

protected void addResult(Object obj)

Description copied from class: RecordParser

Add an object to the results collection.

Specified by:

addResult in class RecordParser<BioSequence>

Parameters:

obj - object