Uses of Class
org.biojava.bio.program.fastq.Fastq

Packages that use Fastq

Package	Description
org.biojava.bio.program.fastq	FASTQ and variants sequence format I/O.

Uses of Fastq in org.biojava.bio.program.fastq

Methods in org.biojava.bio.program.fastq that return Fastq

Modifier and Type	Method	Description
Fastq	FastqBuilder.build()	Build and return a new FASTQ formatted sequence configured from the properties of this builder.
static Fastq	FastqTools.convert(Fastq fastq, FastqVariant variant)	Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.
protected Fastq	IlluminaFastqWriter.convert(Fastq fastq)
protected Fastq	SangerFastqWriter.convert(Fastq fastq)
protected Fastq	SolexaFastqWriter.convert(Fastq fastq)
Fastq	Fastq.convertTo(FastqVariant variant)	Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.

Methods in org.biojava.bio.program.fastq that return types with arguments of type Fastq

Modifier and Type	Method	Description
java.lang.Iterable<Fastq>	FastqReader.read(java.io.File file)	Read zero or more FASTQ formatted sequences from the specified file.
java.lang.Iterable<Fastq>	FastqReader.read(java.io.InputStream inputStream)	Read zero or more FASTQ formatted sequences from the specified input stream.
java.lang.Iterable<Fastq>	FastqReader.read(java.net.URL url)	Read zero or more FASTQ formatted sequences from the specified url.

Methods in org.biojava.bio.program.fastq with parameters of type Fastq

Modifier and Type	Method	Description
<T extends java.lang.Appendable> T	FastqWriter.append(T appendable, Fastq... fastq)	Append the specified FASTQ formatted sequences to the specified appendable.
static FastqBuilder	Fastq.builder(Fastq fastq)	Create and return a new FastqBuilder configured from the specified FASTQ formatted sequence.
static Fastq	FastqTools.convert(Fastq fastq, FastqVariant variant)	Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.
protected Fastq	IlluminaFastqWriter.convert(Fastq fastq)
protected Fastq	SangerFastqWriter.convert(Fastq fastq)
protected Fastq	SolexaFastqWriter.convert(Fastq fastq)
static SymbolList	FastqTools.createDNA(Fastq fastq)	Create and return a new DNA SymbolList from the specified FASTQ formatted sequence.
static Sequence	FastqTools.createDNASequence(Fastq fastq)	Create and return a new DNA Sequence from the specified FASTQ formatted sequence.
static PhredSequence	FastqTools.createPhredSequence(Fastq fastq)	Create and return a new PhredSequence from the specified FASTQ formatted sequence.
static SymbolList	FastqTools.createQualityScores(Fastq fastq)	Create and return a new SymbolList of quality scores from the specified FASTQ formatted sequence.
static Distribution[]	FastqTools.createSymbolDistribution(Fastq fastq)	Create and return a new array of symbol Distributions from the specified FASTQ formatted sequence.
static java.lang.Iterable<java.lang.Double>	FastqTools.errorProbabilities(Fastq fastq)	Return the error probabilities from the specified FASTQ formatted sequence.
static double[]	FastqTools.errorProbabilities(Fastq fastq, double[] errorProbabilities)	Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.
void	StreamListener.fastq(Fastq fastq)	Notify this listener of a FASTQ formatted sequence.
static java.lang.Iterable<java.lang.Integer>	FastqTools.qualityScores(Fastq fastq)	Return the quality scores from the specified FASTQ formatted sequence.
static int[]	FastqTools.qualityScores(Fastq fastq, int[] qualityScores)	Copy the quality scores from the specified FASTQ formatted sequence into the specified int array.
void	FastqWriter.write(java.io.File file, Fastq... fastq)	Write the specified FASTQ formatted sequences to the specified file.
void	FastqWriter.write(java.io.OutputStream outputStream, Fastq... fastq)	Write the specified FASTQ formatted sequences to the specified output stream.

Method parameters in org.biojava.bio.program.fastq with type arguments of type Fastq

Modifier and Type	Method	Description
<T extends java.lang.Appendable> T	FastqWriter.append(T appendable, java.lang.Iterable<Fastq> fastq)	Append the specified FASTQ formatted sequences to the specified appendable.
void	FastqWriter.write(java.io.File file, java.lang.Iterable<Fastq> fastq)	Write the specified FASTQ formatted sequences to the specified file.
void	FastqWriter.write(java.io.OutputStream outputStream, java.lang.Iterable<Fastq> fastq)	Write the specified FASTQ formatted sequences to the specified output stream.

Constructors in org.biojava.bio.program.fastq with parameters of type Fastq

Constructor	Description
FastqBuilder(Fastq fastq)	Create a new FASTQ formatted sequence builder configured from the specified FASTQ formatted sequence.