trans.main
Class ScoreIntervals

java.lang.Object
  trans.main.ScoreIntervals

public class ScoreIntervals

extends java.lang.Object

Scores Intervals for the presence of transcription factor binding sites.

Constructor Summary

ScoreIntervals(java.lang.String[] args)

Method Summary

static void	main(java.lang.String[] args)
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles
void	scanIntervals()
void	setGenomicSequenceParams(Interval interval) Loads up the fasta file for a particular chromosome and sets some params.

Methods inherited from class java.lang.Object

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

Constructor Detail

ScoreIntervals

public ScoreIntervals(java.lang.String[] args)

Method Detail

main

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

printDocs

public static void printDocs()

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign any new varibles

scanIntervals

public void scanIntervals()

setGenomicSequenceParams

public void setGenomicSequenceParams(Interval interval)

Loads up the fasta file for a particular chromosome and sets some params.