Package org.biojava.nbio.sequencing.io.fastq

Class SangerFastqWriter

java.lang.Object
org.biojava.nbio.sequencing.io.fastq.SangerFastqWriter
All Implemented Interfaces:
FastqWriter
public final class SangerFastqWriter extends Object
Writer for FastqVariant.FASTQ_SANGER formatted sequences.
Since:
3.0.3

  • Constructor Details

    • SangerFastqWriter

      public SangerFastqWriter()

  • Method Details

    • convert

      protected Fastq convert(Fastq fastq)
      Convert the specified FASTQ formatted sequence if necessary.
      Parameters:
      fastq - FASTQ formatted sequence to convert, must not be null
      Returns:
      the specified FASTQ formatted sequence or a new FASTA formatted sequence if conversion is necessary

    • append

      public final <T extends Appendable> T append(T appendable, Fastq... fastq) throws IOException
      Description copied from interface: FastqWriter
      Append the specified FASTQ formatted sequences to the specified appendable.
      Specified by:
      append in interface FastqWriter
      Type Parameters:
      T - extends Appendable
      Parameters:
      appendable - appendable to append the specified FASTQ formatted sequences to, must not be null
      fastq - variable number of FASTQ formatted sequences to append, must not be null
      Returns:
      the specified appendable with the specified FASTQ formatted sequences appended
      Throws:
      IOException - if an I/O error occurs

    • append

      public final <T extends Appendable> T append(T appendable, Iterable<Fastq> fastq) throws IOException
      Description copied from interface: FastqWriter
      Append the specified FASTQ formatted sequences to the specified appendable.
      Specified by:
      append in interface FastqWriter
      Type Parameters:
      T - extends Appendable
      Parameters:
      appendable - appendable to append the specified FASTQ formatted sequences to, must not be null
      fastq - zero or more FASTQ formatted sequences to append, must not be null
      Returns:
      the specified appendable with the specified FASTQ formatted sequences appended
      Throws:
      IOException - if an I/O error occurs

    • write

      public final void write(File file, Fastq... fastq) throws IOException
      Description copied from interface: FastqWriter
      Write the specified FASTQ formatted sequences to the specified file.
      Specified by:
      write in interface FastqWriter
      Parameters:
      file - file to write to, must not be null
      fastq - variable number of FASTQ formatted sequences to write, must not be null
      Throws:
      IOException - if an I/O error occurs

    • write

      public final void write(File file, Iterable<Fastq> fastq) throws IOException
      Description copied from interface: FastqWriter
      Write the specified FASTQ formatted sequences to the specified file.
      Specified by:
      write in interface FastqWriter
      Parameters:
      file - file to write to, must not be null
      fastq - zero or more FASTQ formatted sequences to write, must not be null
      Throws:
      IOException - if an I/O error occurs

    • write

      public final void write(OutputStream outputStream, Fastq... fastq) throws IOException
      Description copied from interface: FastqWriter
      Write the specified FASTQ formatted sequences to the specified output stream.
      Specified by:
      write in interface FastqWriter
      Parameters:
      outputStream - output stream to write to, must not be null
      fastq - variable number of FASTQ formatted sequences to write, must not be null
      Throws:
      IOException - if an I/O error occurs

    • write

      public final void write(OutputStream outputStream, Iterable<Fastq> fastq) throws IOException
      Description copied from interface: FastqWriter
      Write the specified FASTQ formatted sequences to the specified output stream.
      Specified by:
      write in interface FastqWriter
      Parameters:
      outputStream - output stream to write to, must not be null
      fastq - zero or more FASTQ formatted sequences to write, must not be null
      Throws:
      IOException - if an I/O error occurs