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 and Description
Fastq	FastqBuilder.build() Build and return a new FASTQ formatted sequence configured from the properties of this builder.

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

Modifier and Type	Method and Description
Iterable<Fastq>	FastqReader.read(File file) Read zero or more FASTQ formatted sequences from the specified file.
Iterable<Fastq>	FastqReader.read(InputStream inputStream) Read zero or more FASTQ formatted sequences from the specified input stream.
Iterable<Fastq>	FastqReader.read(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 and Description
<T extends Appendable> T	FastqWriter.append(T appendable, Fastq... fastq) Append the specified FASTQ formatted sequences to the specified appendable.
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 Iterable<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 Iterable<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.
protected void	SolexaFastqWriter.validate(Fastq fastq) Validate the specified FASTQ formatted sequence for writing.
protected void	SangerFastqWriter.validate(Fastq fastq) Validate the specified FASTQ formatted sequence for writing.
protected void	IlluminaFastqWriter.validate(Fastq fastq) Validate the specified FASTQ formatted sequence for writing.
void	FastqWriter.write(File file, Fastq... fastq) Write the specified FASTQ formatted sequences to the specified file.
void	FastqWriter.write(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 and Description
<T extends Appendable> T	FastqWriter.append(T appendable, Iterable<Fastq> fastq) Append the specified FASTQ formatted sequences to the specified appendable.
void	FastqWriter.write(File file, Iterable<Fastq> fastq) Write the specified FASTQ formatted sequences to the specified file.
void	FastqWriter.write(OutputStream outputStream, Iterable<Fastq> fastq) Write the specified FASTQ formatted sequences to the specified output stream.