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

Packages that use FastqBuilder
org.biojava.bio.program.fastq FASTQ and variants sequence format IO. 
 

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

Methods in org.biojava.bio.program.fastq that return FastqBuilder
 FastqBuilder FastqBuilder.appendQuality(java.lang.String quality)
          Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.
 FastqBuilder FastqBuilder.appendSequence(java.lang.String sequence)
          Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.
 FastqBuilder FastqBuilder.withDescription(java.lang.String description)
          Return this FASTQ formatted sequence builder configured with the specified description.
 FastqBuilder FastqBuilder.withQuality(java.lang.String quality)
          Return this FASTQ formatted sequence builder configured with the specified quality scores.
 FastqBuilder FastqBuilder.withSequence(java.lang.String sequence)
          Return this FASTQ formatted sequence builder configured with the specified sequence.
 FastqBuilder FastqBuilder.withVariant(FastqVariant variant)
          Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.
 

Methods in org.biojava.bio.program.fastq with parameters of type FastqBuilder
protected  void SolexaFastqReader.validateDescription(FastqBuilder builder, java.lang.String description, int lineNumber)
          Validate the specified description.
protected  void SangerFastqReader.validateDescription(FastqBuilder builder, java.lang.String description, int lineNumber)
          Validate the specified description.
protected  void IlluminaFastqReader.validateDescription(FastqBuilder builder, java.lang.String description, int lineNumber)
          Validate the specified description.
protected  void SolexaFastqReader.validateQuality(FastqBuilder builder, java.lang.String quality, int lineNumber)
          Validate the specified quality scores.
protected  void SangerFastqReader.validateQuality(FastqBuilder builder, java.lang.String quality, int lineNumber)
          Validate the specified quality scores.
protected  void IlluminaFastqReader.validateQuality(FastqBuilder builder, java.lang.String quality, int lineNumber)
          Validate the specified quality scores.
protected  void SolexaFastqReader.validateRepeatDescription(FastqBuilder builder, java.lang.String repeatDescription, int lineNumber)
          Validate the specified repeat description.
protected  void SangerFastqReader.validateRepeatDescription(FastqBuilder builder, java.lang.String repeatDescription, int lineNumber)
          Validate the specified repeat description.
protected  void IlluminaFastqReader.validateRepeatDescription(FastqBuilder builder, java.lang.String repeatDescription, int lineNumber)
          Validate the specified repeat description.
protected  void SolexaFastqReader.validateSequence(FastqBuilder builder, java.lang.String sequence, int lineNumber)
          Validate the specified sequence.
protected  void SangerFastqReader.validateSequence(FastqBuilder builder, java.lang.String sequence, int lineNumber)
          Validate the specified sequence.
protected  void IlluminaFastqReader.validateSequence(FastqBuilder builder, java.lang.String sequence, int lineNumber)
          Validate the specified sequence.