uni.bielefeld.cmg.sparkhit.struct

Class ReadInfo

java.lang.Object

uni.bielefeld.cmg.sparkhit.struct.ReadInfo

All Implemented Interfaces:

java.io.Serializable

public class ReadInfo
extends java.lang.Object
implements java.io.Serializable

A data structure class that stores all parameters for a sequence read.

See Also:

, Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	line
java.lang.String	read
java.lang.String	readName
int	readSize

Constructor Summary

Constructors

Constructor and Description
ReadInfo(readInfo r) A constructor that construct an object of ReadInfo class.
ReadInfo(java.lang.String line) A constructor that construct an object of ReadInfo class.

Method Summary

Methods

Modifier and Type	Method and Description
void	logInfo() This method logs all required information from a fastq unit.
void	name(java.lang.String n) This method sets the id of a read.
void	seq(java.lang.String r) This method sets the sequence of a read.
void	size(java.lang.String s) This method sets the length of a sequencing read.

Methods inherited from class java.lang.Object

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

Field Detail

line

public java.lang.String line

readName

public java.lang.String readName

read

public java.lang.String read

readSize

public int readSize

Constructor Detail

ReadInfo

public ReadInfo(java.lang.String line)

A constructor that construct an object of ReadInfo class.

Parameters:

line - the nucleotide sequence of a sequencing read.

ReadInfo

public ReadInfo(readInfo r)

A constructor that construct an object of ReadInfo class.

Parameters:

r - readInfo.

Method Detail

logInfo

public void logInfo()

This method logs all required information from a fastq unit.

name

public void name(java.lang.String n)

This method sets the id of a read.

Parameters:

n - the nucleotide sequence of a read.

seq

public void seq(java.lang.String r)

This method sets the sequence of a read.

Parameters:

r - the nucleotide sequence in a string.

size

public void size(java.lang.String s)

This method sets the length of a sequencing read.

Parameters:

s - the nucleotide sequence of a read.