broad.pda.seq.fastq.FastqSequence Class Reference

Public Member Functions
	FastqSequence (String name, String sequence, String description, String quality)
String	getName ()
String	getSequence ()
String	getDescription ()
void	setName (String name)
void	setDescription (String descr)
String	toString ()
void	write (BufferedWriter bw) throws IOException
void	removeAtSymbolFromName ()
FastqSequence	trimEnds (char letter)
FastqSequence	trimEndBases (int numOfBasesToTrim)
FastqSequence	trimStartBases (int numOfBasesToTrim)
FastqSequence	trimBeginning (char letter)
FastqSequence	trimFirstNBPs (int n)
String	getFirstNBPs (int n)
int	getLength ()
String	toFasta ()
String	toFasta (int readNum)
String	toFastq ()
boolean	isPolyA ()
boolean	isPartialPolyA (int polyN)
FastqSequence	trimPolyA ()
FastqSequence	trimLinker (String linkerSeq)

Constructor & Destructor Documentation

broad.pda.seq.fastq.FastqSequence.FastqSequence	(	String	name,
		String	sequence,
		String	description,
		String	quality
	)

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Member Function Documentation

String broad.pda.seq.fastq.FastqSequence.getDescription

(

)

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String broad.pda.seq.fastq.FastqSequence.getFirstNBPs

(

int

n

)

int broad.pda.seq.fastq.FastqSequence.getLength

(

)

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String broad.pda.seq.fastq.FastqSequence.getName

(

)

String broad.pda.seq.fastq.FastqSequence.getSequence

(

)

boolean broad.pda.seq.fastq.FastqSequence.isPartialPolyA

(

int

polyN

)

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boolean broad.pda.seq.fastq.FastqSequence.isPolyA

(

)

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void broad.pda.seq.fastq.FastqSequence.removeAtSymbolFromName

(

)

void broad.pda.seq.fastq.FastqSequence.setDescription

(

String

descr

)

void broad.pda.seq.fastq.FastqSequence.setName

(

String

name

)

String broad.pda.seq.fastq.FastqSequence.toFasta

(

)

String broad.pda.seq.fastq.FastqSequence.toFasta

(

int

readNum

)

String broad.pda.seq.fastq.FastqSequence.toFastq

(

)

String broad.pda.seq.fastq.FastqSequence.toString

(

)

FastqSequence broad.pda.seq.fastq.FastqSequence.trimBeginning

(

char

letter

)

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FastqSequence broad.pda.seq.fastq.FastqSequence.trimEndBases

(

int

numOfBasesToTrim

)

Trims the last numBasesToTrim bases of the fastq record and returns the nucleotides trimmed.

Parameters

numOfBasesToTrim

Returns

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FastqSequence broad.pda.seq.fastq.FastqSequence.trimEnds

(

char

letter

)

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FastqSequence broad.pda.seq.fastq.FastqSequence.trimFirstNBPs

(

int

n

)

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FastqSequence broad.pda.seq.fastq.FastqSequence.trimLinker

(

String

linkerSeq

)

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FastqSequence broad.pda.seq.fastq.FastqSequence.trimPolyA

(

)

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FastqSequence broad.pda.seq.fastq.FastqSequence.trimStartBases

(

int

numOfBasesToTrim

)

Trims the first numBasesToTrim bases of the fastq record and returns the nucleotides trimmed.

Parameters

numOfBasesToTrim

Returns

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void broad.pda.seq.fastq.FastqSequence.write

(

BufferedWriter

bw

)

throws IOException

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The documentation for this class was generated from the following file:

• java/broad/pda/seq/fastq/FastqSequence.java