A B C D E F G I L M O P Q R S V W

A

append(T, Fastq...) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter

Append the specified FASTQ formatted sequences to the specified appendable.

append(T, Iterable<Fastq>) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter

Append the specified FASTQ formatted sequences to the specified appendable.

appendQuality(String) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.

appendQuality(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this listener of a quality line.

appendSequence(String) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.

appendSequence(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this parse listener of an additional sequence line.

B

build() - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Build and return a new FASTQ formatted sequence configured from the properties of this builder.

builder() - Static method in class org.biojava.nbio.sequencing.io.fastq.Fastq

Create and return a new FastqBuilder.

C

complete() - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this listener the FASTQ formatted sequence is complete.

constrain(double) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Constrain the specified quality score in double precision to the minimum and maximum quality scores in int precision.

convert(Fastq, FastqVariant) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.

convert(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriter

convert(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.SangerFastqWriter

convert(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriter

convertTo(FastqVariant) - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq

Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.

createDNASequence(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Create and return a new DNASequence from the specified FASTQ formatted sequence.

createDNASequenceWithErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Create and return a new DNASequence with error probabilities from the specified FASTQ formatted sequence.

createDNASequenceWithQualityScores(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Create and return a new DNASequence with quality scores from the specified FASTQ formatted sequence.

createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence.

createErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Create and return a new QuantityFeature from the error probabilities of the specified FASTQ formatted sequence.

createQualityScores(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Create and return a new QualityFeature from the quality scores of the specified FASTQ formatted sequence.

D

DEFAULT_VARIANT - Static variable in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Default FASTQ sequence format variant, FastqVariant.FASTQ_SANGER.

description(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this parse listener of a description line.

E

errorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Return the error probabilities from the specified FASTQ formatted sequence.

errorProbabilities(Fastq, double[]) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.

errorProbability(char) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Convert the specified quality in ASCII format to an error probability.

errorProbability(int) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Calculate the error probability given the specified quality score.

F

Fastq - Class in org.biojava.nbio.sequencing.io.fastq

FASTQ formatted sequence.

fastq(Fastq) - Method in interface org.biojava.nbio.sequencing.io.fastq.StreamListener

Notify this listener of a FASTQ formatted sequence.

FastqBuilder - Class in org.biojava.nbio.sequencing.io.fastq

Fluent builder API for creating FASTQ formatted sequences.

FastqBuilder() - Constructor for class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Create a new FASTQ formatted sequence builder.

FastqReader - Interface in org.biojava.nbio.sequencing.io.fastq

Reader for FASTQ formatted sequences.

FastqTools - Class in org.biojava.nbio.sequencing.io.fastq

Utility methods for FASTQ formatted sequences.

FastqVariant - Enum in org.biojava.nbio.sequencing.io.fastq

FASTQ sequence format variant.

FastqWriter - Interface in org.biojava.nbio.sequencing.io.fastq

Writer for FASTQ formatted sequences.

G

getDescription() - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq

Return the description of this FASTQ formatted sequence.

getDescription() - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return the description for this FASTQ formatted sequence builder.

getDescription() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Return the description of this FASTQ sequence format variant.

getQuality() - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq

Return the quality scores for this FASTQ formatted sequence.

getSequence() - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq

Return the sequence for this FASTQ formatted sequence.

getVariant() - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq

Return the FASTQ sequence format variant for this FASTQ formatted sequence.

getVariant() - Method in class org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReader

getVariant() - Method in class org.biojava.nbio.sequencing.io.fastq.SangerFastqReader

getVariant() - Method in class org.biojava.nbio.sequencing.io.fastq.SolexaFastqReader

I

IlluminaFastqReader - Class in org.biojava.nbio.sequencing.io.fastq

Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.

IlluminaFastqReader() - Constructor for class org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReader

IlluminaFastqWriter - Class in org.biojava.nbio.sequencing.io.fastq

Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences.

IlluminaFastqWriter() - Constructor for class org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriter

isIllumina() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_ILLUMINA.

isSanger() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_SANGER.

isSolexa() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_SOLEXA.

L

lowercaseName() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Return the name of this FASTQ sequence format variant in lowercase-with-dashes style.

M

maximumQualityScore() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Return the maximum quality score for this FASTQ sequence format variant.

minimumQualityScore() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Return the minimum quality score for this FASTQ sequence format variant.

O

org.biojava.nbio.sequencing.io.fastq - package org.biojava.nbio.sequencing.io.fastq

FASTQ and variants sequence format I/O.

P

parse(Readable, ParseListener) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqReader

Parse the specified readable.

parseFastqVariant(String) - Static method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Return the FASTQ sequence format variant with the specified name, if any.

ParseListener - Interface in org.biojava.nbio.sequencing.io.fastq

Low-level event based parser callback.

Q

quality(int) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Convert the specified quality score to a quality in ASCII format.

quality(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this listener of a quality line.

qualityScore(char) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Convert the specified quality in ASCII format to a quality score.

qualityScore(double) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Convert the specified error probability to a quality score.

qualityScores(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Return the quality scores from the specified FASTQ formatted sequence.

qualityScores(Fastq, int[]) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Copy the quality scores from the specified FASTQ formatted sequence into the specified int array.

R

read(File) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqReader

Read zero or more FASTQ formatted sequences from the specified file.

read(URL) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqReader

Read zero or more FASTQ formatted sequences from the specified url.

read(InputStream) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqReader

Read zero or more FASTQ formatted sequences from the specified input stream.

repeatDescription(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this parse listener of a repeat description line.

S

SangerFastqReader - Class in org.biojava.nbio.sequencing.io.fastq

Reader for FastqVariant.FASTQ_SANGER formatted sequences.

SangerFastqReader() - Constructor for class org.biojava.nbio.sequencing.io.fastq.SangerFastqReader

SangerFastqWriter - Class in org.biojava.nbio.sequencing.io.fastq

Writer for FastqVariant.FASTQ_SANGER formatted sequences.

SangerFastqWriter() - Constructor for class org.biojava.nbio.sequencing.io.fastq.SangerFastqWriter

sequence(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this parse listener of a sequence line.

sequenceAndQualityLengthsMatch() - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length.

SolexaFastqReader - Class in org.biojava.nbio.sequencing.io.fastq

Reader for FastqVariant.FASTQ_SOLEXA formatted sequences.

SolexaFastqReader() - Constructor for class org.biojava.nbio.sequencing.io.fastq.SolexaFastqReader

SolexaFastqWriter - Class in org.biojava.nbio.sequencing.io.fastq

Writer for FastqVariant.FASTQ_SOLEXA formatted sequences.

SolexaFastqWriter() - Constructor for class org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriter

stream(Readable, StreamListener) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqReader

Stream the specified readable.

StreamListener - Interface in org.biojava.nbio.sequencing.io.fastq

Event based parser callback.

V

valueOf(String) - Static method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Returns an array containing the constants of this enum type, in the order they are declared.

W

withDescription(String) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified description.

withQuality(String) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified quality scores.

withSequence(String) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified sequence.

withVariant(FastqVariant) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.

write(File, Fastq...) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter

Write the specified FASTQ formatted sequences to the specified file.

write(File, Iterable<Fastq>) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter

Write the specified FASTQ formatted sequences to the specified file.

write(OutputStream, Fastq...) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter

Write the specified FASTQ formatted sequences to the specified output stream.

write(OutputStream, Iterable<Fastq>) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter

Write the specified FASTQ formatted sequences to the specified output stream.

A B C D E F G I L M O P Q R S V W