Package org.biojava.nbio.core.sequence.io

Class FastaWriter<S extends Sequence<?>,C extends Compound>

java.lang.Object
org.biojava.nbio.core.sequence.io.FastaWriter<S,C>
public class FastaWriter<S extends Sequence<?>,C extends Compound> extends Object
The FastaWriter writes a collection of sequences to an outputStream. FastaWriterHelper should be used to write out sequences. Each sequence loaded from a fasta file retains the original Fasta header and that is used when writing to the stream. This behavior can be overwritten by implementing a custom FastaHeaderFormatInterface.
Author:
Scooter Willis

  • Constructor Details

  • Method Details

    • setLineSeparator

      public void setLineSeparator(String lineSeparator)
      Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option
      Parameters:
      lineSeparator -

    • process

      public void process() throws IOException
      Throws:
      IOException

    • main

      public static void main(String[] args)

    • getLineLength

      public int getLineLength()
      Returns:
      the lineLength

    • setLineLength

      public void setLineLength(int lineLength)
      Parameters:
      lineLength - the lineLength to set