Uses of Class
org.biojava.nbio.sequencing.io.fastq.Fastq

Packages that use Fastq

Package	Description
org.biojava.nbio.sequencing.io.fastq	FASTQ and variants sequence format I/O.

Uses of Fastq in org.biojava.nbio.sequencing.io.fastq

Methods in org.biojava.nbio.sequencing.io.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.
protected Fastq	SangerFastqWriter.convert(Fastq fastq)
protected Fastq	SolexaFastqWriter.convert(Fastq fastq)
protected Fastq	IlluminaFastqWriter.convert(Fastq fastq)
static Fastq	FastqTools.convert(Fastq fastq, FastqVariant variant) Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.
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.nbio.sequencing.io.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.nbio.sequencing.io.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.
protected Fastq	SangerFastqWriter.convert(Fastq fastq)
protected Fastq	SolexaFastqWriter.convert(Fastq fastq)
protected Fastq	IlluminaFastqWriter.convert(Fastq fastq)
static Fastq	FastqTools.convert(Fastq fastq, FastqVariant variant) Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.
static DNASequence	FastqTools.createDNASequence(Fastq fastq) Create and return a new DNASequence from the specified FASTQ formatted sequence.
static DNASequence	FastqTools.createDNASequenceWithErrorProbabilities(Fastq fastq) Create and return a new DNASequence with error probabilities from the specified FASTQ formatted sequence.
static DNASequence	FastqTools.createDNASequenceWithQualityScores(Fastq fastq) Create and return a new DNASequence with quality scores from the specified FASTQ formatted sequence.
static DNASequence	FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq) Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence.
static QuantityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>	FastqTools.createErrorProbabilities(Fastq fastq) Create and return a new QuantityFeature from the error probabilities of the specified FASTQ formatted sequence.
static QualityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>	FastqTools.createQualityScores(Fastq fastq) Create and return a new QualityFeature from the quality scores of the specified FASTQ formatted sequence.
static Iterable<Number>	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<Number>	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(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.nbio.sequencing.io.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.