org.biojava3.core.sequence.io
Class FastaWriter<S extends Sequence<?>,C extends Compound>

java.lang.Object
  extended by org.biojava3.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 Summary
FastaWriter(OutputStream os, Collection<S> sequences, FastaHeaderFormatInterface<S,C> headerFormat)
          Use default line length of 60
FastaWriter(OutputStream os, Collection<S> sequences, FastaHeaderFormatInterface<S,C> headerFormat, int lineLength)
          Set custom lineLength
 
Method Summary
 int getLineLength()
           
static void main(String[] args)
           
 void process()
           
 void setLineLength(int lineLength)
           
 void setLineSeparator(String lineSeparator)
          Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FastaWriter

public FastaWriter(OutputStream os,
                   Collection<S> sequences,
                   FastaHeaderFormatInterface<S,C> headerFormat)
Use default line length of 60

Parameters:
os -
sequences -
headerFormat -

FastaWriter

public FastaWriter(OutputStream os,
                   Collection<S> sequences,
                   FastaHeaderFormatInterface<S,C> headerFormat,
                   int lineLength)
Set custom lineLength

Parameters:
os -
sequences -
headerFormat -
lineLength -
Method Detail

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 Exception
Throws:
Exception

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