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

Interface FastqWriter

All Known Implementing Classes:
IlluminaFastqWriter, SangerFastqWriter, SolexaFastqWriter
public interface FastqWriter
Writer for FASTQ formatted sequences.
Since:
3.0.3

  • Method Summary

    Modifier and Type
    Method
    Description
    <T extends Appendable>
    T
    append(T appendable, Iterable<Fastq> fastq)
    Append the specified FASTQ formatted sequences to the specified appendable.
    <T extends Appendable>
    T
    append(T appendable, Fastq... fastq)
    Append the specified FASTQ formatted sequences to the specified appendable.
    void
    write(File file, Iterable<Fastq> fastq)
    Write the specified FASTQ formatted sequences to the specified file.
    void
    write(File file, Fastq... fastq)
    Write the specified FASTQ formatted sequences to the specified file.
    void
    write(OutputStream outputStream, Iterable<Fastq> fastq)
    Write the specified FASTQ formatted sequences to the specified output stream.
    void
    write(OutputStream outputStream, Fastq... fastq)
    Write the specified FASTQ formatted sequences to the specified output stream.

  • Method Details

    • append

      <T extends Appendable> T append(T appendable, Fastq... fastq) throws IOException
      Append the specified FASTQ formatted sequences to the specified appendable.
      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

      <T extends Appendable> T append(T appendable, Iterable<Fastq> fastq) throws IOException
      Append the specified FASTQ formatted sequences to the specified appendable.
      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

      void write(File file, Fastq... fastq) throws IOException
      Write the specified FASTQ formatted sequences to the specified file.
      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

      void write(File file, Iterable<Fastq> fastq) throws IOException
      Write the specified FASTQ formatted sequences to the specified file.
      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

      void write(OutputStream outputStream, Fastq... fastq) throws IOException
      Write the specified FASTQ formatted sequences to the specified output stream.
      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

      void write(OutputStream outputStream, Iterable<Fastq> fastq) throws IOException
      Write the specified FASTQ formatted sequences to the specified output stream.
      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