Package org.biojava.nbio.genome.io.fastq

Class SangerFastqWriter

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      <T extends java.lang.Appendable>
      T      		 append​(T appendable, java.lang.Iterable<Fastq> fastq)
      Append the specified FASTQ formatted sequences to the specified appendable.
      <T extends java.lang.Appendable>
      T      		 append​(T appendable, Fastq... fastq)
      Append the specified FASTQ formatted sequences to the specified appendable.
      protected Fastq convert​(Fastq fastq)
      Convert the specified FASTQ formatted sequence if necessary.
      void write​(java.io.File file, java.lang.Iterable<Fastq> fastq)
      Write the specified FASTQ formatted sequences to the specified file.
      void write​(java.io.File file, Fastq... fastq)
      Write the specified FASTQ formatted sequences to the specified file.
      void write​(java.io.OutputStream outputStream, java.lang.Iterable<Fastq> fastq)
      Write the specified FASTQ formatted sequences to the specified output stream.
      void write​(java.io.OutputStream outputStream, Fastq... fastq)
      Write the specified FASTQ formatted sequences to the specified output stream.

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • SangerFastqWriter

        public SangerFastqWriter()

    • Method Detail

      • 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 java.lang.Appendable> T append​(T appendable,
                                                       Fastq... fastq)
                                                throws java.io.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:
        java.io.IOException - if an I/O error occurs

      • append

        public final <T extends java.lang.Appendable> T append​(T appendable,
                                                       java.lang.Iterable<Fastq> fastq)
                                                throws java.io.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:
        java.io.IOException - if an I/O error occurs

      • write

        public final void write​(java.io.File file,
                        Fastq... fastq)
                 throws java.io.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:
        java.io.IOException - if an I/O error occurs

      • write

        public final void write​(java.io.File file,
                        java.lang.Iterable<Fastq> fastq)
                 throws java.io.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:
        java.io.IOException - if an I/O error occurs

      • write

        public final void write​(java.io.OutputStream outputStream,
                        Fastq... fastq)
                 throws java.io.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:
        java.io.IOException - if an I/O error occurs

      • write

        public final void write​(java.io.OutputStream outputStream,
                        java.lang.Iterable<Fastq> fastq)
                 throws java.io.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:
        java.io.IOException - if an I/O error occurs