Class Pileup

java.lang.Object
  Pileup

public class Pileup
extends java.lang.Object

Class to handle pileup files

Author:

arthiramachandran

Field Summary

(package private) int	chromosome
(package private) int	coverage
(package private) int	heterozygous
(package private) int	homozygous
(package private) int	position

Constructor Summary

Pileup(java.lang.String line)

Method Summary

static void	readData(java.util.ArrayList<Exon> exons, java.io.BufferedReader br) Reads the pileup and simultaneously updates the exon lists with appropriate values
static java.util.HashMap<java.lang.Integer,Pileup>	readData(java.io.BufferedReader br) Reads and parses the pileup file
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

position

int position

heterozygous

int heterozygous

homozygous

int homozygous

coverage

int coverage

chromosome

int chromosome

Constructor Detail

Pileup

public Pileup(java.lang.String line)

Method Detail

readData

public static java.util.HashMap<java.lang.Integer,Pileup> readData(java.io.BufferedReader br)

Reads and parses the pileup file

Parameters:

br - buffered reader to the pileup file

Returns:

hashmap of the pileups

readData

public static void readData(java.util.ArrayList<Exon> exons,
                            java.io.BufferedReader br)

Reads the pileup and simultaneously updates the exon lists with appropriate values

Parameters:

exons - list of exons to be populated with values from the pileup

br - buffered reader to pileup file

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object