org.kepler.bio.hadoop.input

Class FASTAInputFormat

java.lang.Object

org.apache.hadoop.mapreduce.InputFormat<K,V>

org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

org.kepler.bio.hadoop.input.FASTAInputFormat

public class FASTAInputFormat
extends org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

This class extend FileInputFormat class to read multiple sequence in each map function. The sequence number for each reader is configurable through DDPSource parameter: SequenceNumberPerExecution.

Author:

Jianwu Wang (jianwu@sdsc.edu)

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat

org.apache.hadoop.mapreduce.lib.input.FileInputFormat.Counter

Field Summary

Fields inherited from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat

INPUT_DIR, INPUT_DIR_RECURSIVE, NUM_INPUT_FILES, PATHFILTER_CLASS, SPLIT_MAXSIZE, SPLIT_MINSIZE

Constructor Summary

Constructors

Constructor and Description
FASTAInputFormat()

Method Summary

Modifier and Type	Method and Description
org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>	createRecordReader(org.apache.hadoop.mapreduce.InputSplit split, org.apache.hadoop.mapreduce.TaskAttemptContext context)
java.util.List<org.apache.hadoop.mapreduce.InputSplit>	getSplits(org.apache.hadoop.mapreduce.JobContext job)

Methods inherited from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat

addInputPath, addInputPathRecursively, addInputPaths, computeSplitSize, getBlockIndex, getFormatMinSplitSize, getInputDirRecursive, getInputPathFilter, getInputPaths, getMaxSplitSize, getMinSplitSize, isSplitable, listStatus, makeSplit, setInputDirRecursive, setInputPathFilter, setInputPaths, setInputPaths, setMaxInputSplitSize, setMinInputSplitSize

Methods inherited from class java.lang.Object

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

Constructor Detail

FASTAInputFormat

public FASTAInputFormat()

Method Detail

createRecordReader

public org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text> createRecordReader(org.apache.hadoop.mapreduce.InputSplit split,
                                                                                                                        org.apache.hadoop.mapreduce.TaskAttemptContext context)

Specified by:

createRecordReader in class org.apache.hadoop.mapreduce.InputFormat<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

getSplits

public java.util.List<org.apache.hadoop.mapreduce.InputSplit> getSplits(org.apache.hadoop.mapreduce.JobContext job)
                                                                 throws java.io.IOException

Overrides:

getSplits in class org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

java.io.IOException