org.biojavax.bio.seq.io

Class RichStreamWriter

java.lang.Object

org.biojavax.bio.seq.io.RichStreamWriter

public class RichStreamWriter
extends java.lang.Object

Writes all of the sequences from a SequenceIterator to a stream with a particular format. This can be wired from a StreamReader to make a simple file-format conversion utility, or can be used to write out the sequences in a database to disk.

Since:

1.5

Author:

Matthew Pocock, Richard Holland

Constructor Summary

Constructors

Constructor and Description
RichStreamWriter(java.io.OutputStream os, RichSequenceFormat format) Generate a new RichStreamWriter to the stream os and using format.

Method Summary

Methods

Modifier and Type	Method and Description
void	writeStream(SequenceIterator ss, Namespace ns) Write each of the sequences in ss to the stream in the given format.

Methods inherited from class java.lang.Object

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

Constructor Detail

RichStreamWriter

public RichStreamWriter(java.io.OutputStream os,
                RichSequenceFormat format)

Generate a new RichStreamWriter to the stream os and using format.

Parameters:

os - the OutputStream to write to

format - the SequenceFormat to write with

Method Detail

writeStream

public void writeStream(SequenceIterator ss,
               Namespace ns)
                 throws java.io.IOException

Write each of the sequences in ss to the stream in the given format.

Parameters:

ss - the SequenceIterator to loop over

Throws:

java.io.IOException - if the stream has any problems