Package fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop

Class PreTreatmentExpressionMapper

java.lang.Object

org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.LongWritable,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionMapper

public class PreTreatmentExpressionMapper
extends org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.LongWritable,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

This class define a mapper for the pretreatment of paired-end data before the expression estimation step.

Since:

1.2

Author:

Claire Wallon

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.hadoop.mapreduce.Mapper

org.apache.hadoop.mapreduce.Mapper.Context

Constructor Summary

Constructors

Constructor	Description
PreTreatmentExpressionMapper()

Method Summary

Modifier and Type	Method	Description
protected void	cleanup(org.apache.hadoop.mapreduce.Mapper.Context context)
protected void	map(org.apache.hadoop.io.LongWritable key, org.apache.hadoop.io.Text value, org.apache.hadoop.mapreduce.Mapper.Context context)
protected void	setup(org.apache.hadoop.mapreduce.Mapper.Context context)

Methods inherited from class org.apache.hadoop.mapreduce.Mapper

run

Methods inherited from class java.lang.Object

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

Constructor Detail

PreTreatmentExpressionMapper

public PreTreatmentExpressionMapper()

Method Detail

setup

protected void setup(org.apache.hadoop.mapreduce.Mapper.Context context)
              throws IOException,
                     InterruptedException

Overrides:

setup in class org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.LongWritable,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException

map

protected void map(org.apache.hadoop.io.LongWritable key,
                   org.apache.hadoop.io.Text value,
                   org.apache.hadoop.mapreduce.Mapper.Context context)
            throws IOException,
                   InterruptedException

Overrides:

map in class org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.LongWritable,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException

cleanup

protected void cleanup(org.apache.hadoop.mapreduce.Mapper.Context context)
                throws IOException,
                       InterruptedException

Overrides:

cleanup in class org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.LongWritable,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException