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

Interface FastqReader

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      void parse​(java.lang.Readable readable, ParseListener listener)
      Parse the specified readable.
      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.
      void stream​(java.lang.Readable readable, StreamListener listener)
      Stream the specified readable.

    • Method Detail

      • parse

        void parse​(java.lang.Readable readable,
           ParseListener listener)
    throws java.io.IOException
        Parse the specified readable.
        Parameters:
        readable - readable, must not be null
        listener - low-level event based parser callback, must not be null
        Throws:
        java.io.IOException - if an I/O error occurs

      • stream

        void stream​(java.lang.Readable readable,
            StreamListener listener)
     throws java.io.IOException
        Stream the specified readable.
        Parameters:
        readable - readable, must not be null
        listener - event based reader callback, must not be null
        Throws:
        java.io.IOException - if an I/O error occurs

      • read

        java.lang.Iterable<Fastq> read​(java.io.File file)
                        throws java.io.IOException
        Read zero or more FASTQ formatted sequences from the specified file.
        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 I/O error occurs

      • read

        java.lang.Iterable<Fastq> read​(java.net.URL url)
                        throws java.io.IOException
        Read zero or more FASTQ formatted sequences from the specified url.
        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 I/O error occurs

      • read

        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.
        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 I/O error occurs