Class CONDR

java.lang.Object
  CONDR

public class CONDR
extends java.lang.Object

Main calling function of program Gets data; parses it; computes most likely states

Author:

arthiramachandran

Field Summary

(package private) static java.util.ArrayList<java.lang.String>	baselineExonFileNames
(package private) static java.util.ArrayList<java.lang.Integer>	chromosomes
(package private) static java.lang.String	exonFileName
(package private) static java.util.ArrayList<Exon>	Exons
(package private) static java.util.ArrayList<Exon>	ExpectedValues
(package private) static java.lang.String	outputFileName
(package private) static java.lang.String	parameterFileName
(package private) static boolean	printTimingMetrics
(package private) static java.util.ArrayList<Exon>	StdDeviations
(package private) static double	threshold
(package private) static boolean	usingPileup

Constructor Summary

CONDR()

Method Summary

static void	main(java.lang.String[] args)
private static void	parseArguments(java.lang.String[] arguments) Parses arguments to program

Methods inherited from class java.lang.Object

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

Field Detail

Exons

static java.util.ArrayList<Exon> Exons

ExpectedValues

static java.util.ArrayList<Exon> ExpectedValues

StdDeviations

static java.util.ArrayList<Exon> StdDeviations

exonFileName

static java.lang.String exonFileName

outputFileName

static java.lang.String outputFileName

baselineExonFileNames

static java.util.ArrayList<java.lang.String> baselineExonFileNames

chromosomes

static java.util.ArrayList<java.lang.Integer> chromosomes

parameterFileName

static java.lang.String parameterFileName

printTimingMetrics

static boolean printTimingMetrics

usingPileup

static boolean usingPileup

threshold

static double threshold

Constructor Detail

CONDR

public CONDR()

Method Detail

main

public static void main(java.lang.String[] args)

parseArguments

private static void parseArguments(java.lang.String[] arguments)

Parses arguments to program

Parameters:

arguments - list of arguments