org.kepler.bio.hadoop.input

Class FASTARecordReader

java.lang.Object

org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

org.kepler.bio.hadoop.input.FASTARecordReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class FASTARecordReader
extends org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

This class treats keys as file paths and value as sequence. The class is modified based on class org.apache.hadoop.mapreduce.lib.input.LineRecordReader.

Author:

Jianwu Wang (jianwu@sdsc.edu)

Constructor Summary

Constructors

Constructor and Description
FASTARecordReader()

Method Summary

Modifier and Type	Method and Description
void	close()
org.apache.hadoop.io.Text	getCurrentKey()
org.apache.hadoop.io.Text	getCurrentValue()
float	getProgress() Get the progress within the split
void	initialize(org.apache.hadoop.mapreduce.InputSplit genericSplit, org.apache.hadoop.mapreduce.TaskAttemptContext context)
boolean	nextKeyValue()

Methods inherited from class java.lang.Object

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

Constructor Detail

FASTARecordReader

public FASTARecordReader()

Method Detail

initialize

public void initialize(org.apache.hadoop.mapreduce.InputSplit genericSplit,
                       org.apache.hadoop.mapreduce.TaskAttemptContext context)
                throws java.io.IOException

Specified by:

initialize in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

java.io.IOException

nextKeyValue

public boolean nextKeyValue()
                     throws java.io.IOException

Specified by:

nextKeyValue in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

java.io.IOException

getCurrentKey

public org.apache.hadoop.io.Text getCurrentKey()

Specified by:

getCurrentKey in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

getCurrentValue

public org.apache.hadoop.io.Text getCurrentValue()

Specified by:

getCurrentValue in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

getProgress

public float getProgress()

Get the progress within the split

Specified by:

getProgress in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

java.io.IOException