trans.roc
Class ParseBarsForParticularRegions

java.lang.Object
  trans.roc.ParseBarsForParticularRegions

public class ParseBarsForParticularRegions

extends java.lang.Object

Returns oligo values that overlap particular regions.

Constructor Summary

ParseBarsForParticularRegions(java.lang.String[] args)

Method Summary

double	calculateFractionGCContent(int start, int stop) Calculates the gc content.
static int	inRegion(Sgr sgr, Positive[] pos) Checks to see if an sgr object is in one of the positives, if not returns -1, otherwise returns index number.
void	loadChromosomeBarFile()
void	loadRegion(Positive region) Loads a Positive with Gr objects.
static void	main(java.lang.String[] args)
void	makeRandom(Positive region, double numberScores) Takes a Positive and finds 1000 chrom, length, gc, and number scores matched random regions.
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles

Methods inherited from class java.lang.Object

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

Constructor Detail

ParseBarsForParticularRegions

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

Method Detail

makeRandom

public void makeRandom(Positive region,
                       double numberScores)

Takes a Positive and finds 1000 chrom, length, gc, and number scores matched random regions. Calculates each mean and sets in the Positive.

calculateFractionGCContent

public double calculateFractionGCContent(int start,
                                         int stop)

Calculates the gc content.

loadChromosomeBarFile

public void loadChromosomeBarFile()

inRegion

public static int inRegion(Sgr sgr,
                           Positive[] pos)

Checks to see if an sgr object is in one of the positives, if not returns -1, otherwise returns index number.

loadRegion

public void loadRegion(Positive region)

Loads a Positive with Gr objects.

main

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

processArgs

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

This method will process each argument and assign new varibles

printDocs

public static void printDocs()