com.hfg.bio.seq.format

Class FASTQ<T extends NucleicAcid>

java.lang.Object

com.hfg.bio.seq.format.ReadableSeqFormatBase<T>

com.hfg.bio.seq.format.FASTQ<T>

All Implemented Interfaces:

ReadableSeqFormat<T>, WritableSeqFormat<T>

Direct Known Subclasses:

IlluminaFASTQ

public class FASTQ<T extends NucleicAcid>
extends ReadableSeqFormatBase<T>
implements WritableSeqFormat<T>

FASTQ sequence format encompassing sequences and their per-base sequencing quality scores.

From Wikipedia:

 "A FASTQ file normally uses four lines per sequence.

 Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).
 Line 2 is the raw sequence letters.
 Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.
 Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence."
 

Constructor Summary

Constructors

Constructor and Description
FASTQ()
FASTQ(BioSequenceFactory<T> inSeqFactory)

Method Summary

Modifier and Type	Method and Description
SeqQualityScoreScheme	getScheme()
boolean	hasJanusDelimiter() A format has a Janus delimiter if the line that indicates that the previous record is over is also part of the next record.
boolean	isEndOfRecord(String inLine)
protected void	parseHeaderLine(String inLine, T inSeq)
T	readRecord(BufferedReader inReader)
FASTQ<T>	setScheme(SeqQualityScoreScheme inValue)
String	write(T inSeq)
void	write(T inSeq, OutputStream inStream)
void	write(T inSeq, Writer inWriter)

Methods inherited from class com.hfg.bio.seq.format.ReadableSeqFormatBase

getBioSequenceFactory, read, read, readRecord

Methods inherited from class java.lang.Object

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

Constructor Detail

FASTQ

public FASTQ()

FASTQ

public FASTQ(BioSequenceFactory<T> inSeqFactory)

Method Detail

setScheme

public FASTQ<T> setScheme(SeqQualityScoreScheme inValue)

getScheme

public SeqQualityScoreScheme getScheme()

readRecord

public T readRecord(BufferedReader inReader)
             throws SeqIOException

Specified by:

readRecord in interface ReadableSeqFormat<T extends NucleicAcid>

Throws:

SeqIOException

isEndOfRecord

public boolean isEndOfRecord(String inLine)

Specified by:

isEndOfRecord in interface ReadableSeqFormat<T extends NucleicAcid>

hasJanusDelimiter

public boolean hasJanusDelimiter()

Description copied from interface: ReadableSeqFormat

A format has a Janus delimiter if the line that indicates that the previous record is over is also part of the next record. Will return true for formats like FASTA.

Specified by:

hasJanusDelimiter in interface ReadableSeqFormat<T extends NucleicAcid>

Returns:

whether or not this format's record delimiter is also part of the next record

write

public String write(T inSeq)
             throws SeqIOException

Specified by:

write in interface WritableSeqFormat<T extends NucleicAcid>

Throws:

SeqIOException

write

public void write(T inSeq,
                  OutputStream inStream)
           throws SeqIOException

Throws:

SeqIOException

write

public void write(T inSeq,
                  Writer inWriter)
           throws SeqIOException

Specified by:

write in interface WritableSeqFormat<T extends NucleicAcid>

Throws:

SeqIOException

parseHeaderLine

protected void parseHeaderLine(String inLine,
                               T inSeq)