Inheritance diagram for broad.pda.seq.fastq.FastqParser:

Collaboration diagram for broad.pda.seq.fastq.FastqParser:

Public Member Functions
	FastqParser (File fastqFile) throws IOException

	FastqParser ()

void	start (File fastqParser) throws IOException

void	start (BufferedReader br) throws IOException

void	convertToFasta (String save) throws IOException

void	convertToNumberedFasta (String save) throws IOException

Collection< FastqSequence >	parse (File file) throws IOException

Collection< FastqSequence >	getSequences () throws IOException

File[]	writeChunks (String save, int chunkSize) throws IOException

int	getNumberOfSequences ()

boolean	hasNext ()

FastqSequence	next ()

void	close () throws IOException

void	remove ()

Constructor & Destructor Documentation

broad.pda.seq.fastq.FastqParser.FastqParser ( File fastqFile ) throws IOException

This constructure is highly discouraged as it opens a reader. Use the empty constructor instead and set the file to read, then call start.

Parameters

fastqFile

Exceptions

IOException

broad.pda.seq.fastq.FastqParser.FastqParser ( )

Member Function Documentation

void broad.pda.seq.fastq.FastqParser.close ( ) throws IOException

void broad.pda.seq.fastq.FastqParser.convertToFasta ( String save ) throws IOException

void broad.pda.seq.fastq.FastqParser.convertToNumberedFasta ( String save ) throws IOException

int broad.pda.seq.fastq.FastqParser.getNumberOfSequences ( )

Collection<FastqSequence> broad.pda.seq.fastq.FastqParser.getSequences ( ) throws IOException

boolean broad.pda.seq.fastq.FastqParser.hasNext ( )

FastqSequence broad.pda.seq.fastq.FastqParser.next ( )

Collection<FastqSequence> broad.pda.seq.fastq.FastqParser.parse ( File file ) throws IOException

void broad.pda.seq.fastq.FastqParser.remove ( )

void broad.pda.seq.fastq.FastqParser.start ( File fastqParser ) throws IOException

void broad.pda.seq.fastq.FastqParser.start ( BufferedReader br ) throws IOException

File [] broad.pda.seq.fastq.FastqParser.writeChunks	(	String	save,
		int	chunkSize
	)		throws IOException

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