org.biojava.bio.program.fastq

Class IlluminaFastqReader

java.lang.Object

org.biojava.bio.program.fastq.IlluminaFastqReader

All Implemented Interfaces:

FastqReader

public final class IlluminaFastqReader
extends java.lang.Object

Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.

Constructor Summary

Constructors

Constructor and Description
IlluminaFastqReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected FastqVariant	getVariant() Return the FASTQ sequence format variant for this reader.
java.lang.Iterable<Fastq>	read(java.io.File file) Read zero or more FASTQ formatted sequences from the specified file.
java.lang.Iterable<Fastq>	read(java.io.InputStream inputStream) Read zero or more FASTQ formatted sequences from the specified input stream.
java.lang.Iterable<Fastq>	read(java.net.URL url) Read zero or more FASTQ formatted sequences from the specified url.
protected void	validateDescription(FastqBuilder builder, java.lang.String description, int lineNumber) Validate the specified description.
protected void	validateQuality(FastqBuilder builder, java.lang.String quality, int lineNumber) Validate the specified quality scores.
protected void	validateRepeatDescription(FastqBuilder builder, java.lang.String repeatDescription, int lineNumber) Validate the specified repeat description.
protected void	validateSequence(FastqBuilder builder, java.lang.String sequence, int lineNumber) Validate the specified sequence.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

IlluminaFastqReader

public IlluminaFastqReader()

Method Detail

getVariant

protected FastqVariant getVariant()

Return the FASTQ sequence format variant for this reader.

Returns:

the FASTQ sequence format variant for this reader

validateDescription

protected void validateDescription(FastqBuilder builder,
                       java.lang.String description,
                       int lineNumber)
                            throws java.io.IOException

Validate the specified description.

Parameters:

builder - FASTQ formatted sequence builder, will not be null

description - description to validate, will not be null

lineNumber - current line number in input stream

Throws:

java.io.IOException - if the specified description is not valid

validateSequence

protected void validateSequence(FastqBuilder builder,
                    java.lang.String sequence,
                    int lineNumber)
                         throws java.io.IOException

Validate the specified sequence.

Parameters:

builder - FASTQ formatted sequence builder, will not be null

sequence - sequence to validate, will not be null

lineNumber - current line number in input stream

Throws:

java.io.IOException - if the specified sequence is not valid

validateRepeatDescription

protected void validateRepeatDescription(FastqBuilder builder,
                             java.lang.String repeatDescription,
                             int lineNumber)
                                  throws java.io.IOException

Validate the specified repeat description.

Parameters:

builder - FASTQ formatted sequence builder, will not be null

repeatDescription - repeat description to validate, will not be null

lineNumber - current line number in input stream

Throws:

java.io.IOException - if the specified repeat description is not valid

validateQuality

protected void validateQuality(FastqBuilder builder,
                   java.lang.String quality,
                   int lineNumber)
                        throws java.io.IOException

Validate the specified quality scores.

Parameters:

builder - FASTQ formatted sequence builder, will not be null

quality - quality scores to validate, will not be null

lineNumber - current line number in input stream

Throws:

java.io.IOException - if the specified quality scores are not valid

read

public final java.lang.Iterable<Fastq> read(java.io.File file)
                                     throws java.io.IOException

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

Specified by:

read in interface FastqReader

Parameters:

file - file to read from, must not be null

Returns:

zero or more FASTQ formatted sequences read from the specified file

Throws:

java.io.IOException - if an IO error occurs

read

public final java.lang.Iterable<Fastq> read(java.net.URL url)
                                     throws java.io.IOException

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

Specified by:

read in interface FastqReader

Parameters:

url - URL to read from, must not be null

Returns:

zero or more FASTQ formatted sequences read from the specified url

Throws:

java.io.IOException - if an IO error occurs

read

public final java.lang.Iterable<Fastq> read(java.io.InputStream inputStream)
                                     throws java.io.IOException

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

Specified by:

read in interface FastqReader

Parameters:

inputStream - input stream to read from, must not be null

Returns:

zero or more FASTQ formatted sequences read from the specified input stream

Throws:

java.io.IOException - if an IO error occurs