org.kepler.bio.hadoop.input

Class FASTAFileReader

java.lang.Object

org.kepler.bio.hadoop.input.FASTAFileReader

public class FASTAFileReader
extends java.lang.Object

A class that provides a multiple sequence reader from an input stream. The sequence number for each reader is configurable through KEPLER::parameter::SequenceNumberPerExecution parameter which can be set in DDPDataSource actor. The class is modified based on class org.apache.hadoop.util.LineReader.

Author:

Jianwu Wang (jianwu@sdsc.edu)

Constructor Summary

Constructors

Constructor and Description
FASTAFileReader(java.io.InputStream in) Create a line reader that reads from the given stream using the default buffer-size (64k).
FASTAFileReader(java.io.InputStream in, org.apache.hadoop.conf.Configuration conf) Create a line reader that reads from the given stream using the io.file.buffer.size specified in the given Configuration.
FASTAFileReader(java.io.InputStream in, int bufferSize) Create a line reader that reads from the given stream using the given buffer-size.

Method Summary

Modifier and Type	Method and Description
void	close() Close the underlying stream.
int	readSequence(org.apache.hadoop.io.Text str) Read from the InputStream into the given Text.
int	readSequence(org.apache.hadoop.io.Text str, int maxBytesToConsume, int seqNumber) Read one line from the InputStream into the given Text.

Methods inherited from class java.lang.Object

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

Constructor Detail

FASTAFileReader

public FASTAFileReader(java.io.InputStream in)

Create a line reader that reads from the given stream using the default buffer-size (64k).

Parameters:

in - The input stream

Throws:

java.io.IOException

FASTAFileReader

public FASTAFileReader(java.io.InputStream in,
                       int bufferSize)

Create a line reader that reads from the given stream using the given buffer-size.

Parameters:

in - The input stream

bufferSize - Size of the read buffer

Throws:

java.io.IOException

FASTAFileReader

public FASTAFileReader(java.io.InputStream in,
                       org.apache.hadoop.conf.Configuration conf)
                throws java.io.IOException

Create a line reader that reads from the given stream using the io.file.buffer.size specified in the given Configuration.

Parameters:

in - input stream

conf - configuration

Throws:

java.io.IOException

Method Detail

close

public void close()
           throws java.io.IOException

Close the underlying stream.

Throws:

java.io.IOException

readSequence

public int readSequence(org.apache.hadoop.io.Text str,
                        int maxBytesToConsume,
                        int seqNumber)
                 throws java.io.IOException

Read one line from the InputStream into the given Text. A line can be terminated by '>'. EOF also terminates an otherwise unterminated line.

Parameters:

str - the object to store the given line (without newline)

maxBytesToConsume - the maximum number of bytes to consume in this call. This is only a hint, because if the line cross this threshold, we allow it to happen. It can overshoot potentially by as much as one buffer length.

seqNumber - sequence number for each key value record. It is read from configuration file if it is null.

Returns:

the number of bytes read including the (longest) newline found.

Throws:

java.io.IOException - if the underlying stream throws

readSequence

public int readSequence(org.apache.hadoop.io.Text str)
                 throws java.io.IOException

Read from the InputStream into the given Text.

Parameters:

str - the object to store the given line

Returns:

the number of bytes read including the newline

Throws:

java.io.IOException - if the underlying stream throws