org.seqdoop.hadoop_bam

Class ReferenceFragment

java.lang.Object

org.seqdoop.hadoop_bam.ReferenceFragment

All Implemented Interfaces:

org.apache.hadoop.io.Writable

public class ReferenceFragment
extends Object
implements org.apache.hadoop.io.Writable

Field Summary

Fields

Modifier and Type	Field and Description
protected String	indexSequence
protected Integer	position
protected org.apache.hadoop.io.Text	sequence

Constructor Summary

Constructors

Constructor and Description
ReferenceFragment()

Method Summary

Modifier and Type	Method and Description
void	clear()
boolean	equals(Object other)
String	getIndexSequence()
Integer	getPosition()
org.apache.hadoop.io.Text	getSequence() Get sequence Text object.
int	hashCode()
void	readFields(DataInput in)
void	setIndexSequence(String v)
void	setPosition(Integer pos) Get quality Text object.
void	setSequence(org.apache.hadoop.io.Text seq)
String	toString() Recreates a pseudo fasta record with the fields available.
void	write(DataOutput out)

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

sequence

protected org.apache.hadoop.io.Text sequence

position

protected Integer position

indexSequence

protected String indexSequence

Constructor Detail

ReferenceFragment

public ReferenceFragment()

Method Detail

clear

public void clear()

getSequence

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

Get sequence Text object. Trade encapsulation for efficiency. Here we expose the internal Text object so that data may be read and written diretly from/to it. Sequence should always be written using CAPITAL letters and 'N' for unknown bases.

setPosition

public void setPosition(Integer pos)

Get quality Text object. Trade encapsulation for efficiency. Here we expose the internal Text object so that data may be read and written diretly from/to it.

setIndexSequence

public void setIndexSequence(String v)

setSequence

public void setSequence(org.apache.hadoop.io.Text seq)

getPosition

public Integer getPosition()

getIndexSequence

public String getIndexSequence()

toString

public String toString()

Recreates a pseudo fasta record with the fields available.

Overrides:

toString in class Object

equals

public boolean equals(Object other)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

readFields

public void readFields(DataInput in)
                throws IOException

Specified by:

readFields in interface org.apache.hadoop.io.Writable

Throws:

IOException

write

public void write(DataOutput out)
           throws IOException

Specified by:

write in interface org.apache.hadoop.io.Writable

Throws:

IOException