trans.roc
Class MethodTester

java.lang.Object
  trans.roc.MethodTester

public class MethodTester

extends java.lang.Object

Application for scoring '.sgr' files for positives and negatives in relation to known (spike in) data.

Constructor Summary

MethodTester(java.lang.String[] args)

Method Summary

void	binSgrs() Runs through an array of Sgr[] noting whether it falls in the positive regions or not positive regions
void	blankPositives() Resets the positive regions to their instantiation state.
void	calculateBinFDRs() Runs through all the bins calculating and setting fdrs for each.
Bin	findBin(Sgr sgr) Finds an appropriate bin given an sgr object
static double	fractionPositive(java.util.ArrayList doubles, double scoreCutOff, double divider) Given an ArrayList of Double, calculates the fraction that is >= scoreCutOff.
static void	main(java.lang.String[] args)
void	makeBins()
void	makePositives()
void	makePositives(java.io.File regions)
static Sgr[]	parseSgrFile(java.io.File sgrFile, boolean zeroNaNOrInfinityScores) Reads in an Sgr file.
static int	positive(Positive[] pos, Sgr sgr) Checks to see if an sgr object is one of the positives, if not returns -1, otherwise returns index number.
boolean	resetStartStop() Scans the bins to determine the optimal start and stop for the next round.

Methods inherited from class java.lang.Object

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

Constructor Detail

MethodTester

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

Method Detail

calculateBinFDRs

public void calculateBinFDRs()

Runs through all the bins calculating and setting fdrs for each.

binSgrs

public void binSgrs()

Runs through an array of Sgr[] noting whether it falls in the positive regions or not positive regions

positive

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

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

findBin

public Bin findBin(Sgr sgr)

Finds an appropriate bin given an sgr object

main

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

fractionPositive

public static double fractionPositive(java.util.ArrayList doubles,
                                      double scoreCutOff,
                                      double divider)

Given an ArrayList of Double, calculates the fraction that is >= scoreCutOff.

makeBins

public void makeBins()

makePositives

public void makePositives()

blankPositives

public void blankPositives()

Resets the positive regions to their instantiation state.

makePositives

public void makePositives(java.io.File regions)

parseSgrFile

public static Sgr[] parseSgrFile(java.io.File sgrFile,
                                 boolean zeroNaNOrInfinityScores)

Reads in an Sgr file. Chrom, position, score. Returns null if not a number or infinity is found and the zero flag is false.

resetStartStop

public boolean resetStartStop()

Scans the bins to determine the optimal start and stop for the next round. Returns true if start and stop were reset and another round should be run. Returns false if not reset.