ubic.erminej.data

Class Histogram

java.lang.Object

ubic.erminej.data.Histogram

public class Histogram
extends Object

Stores distributions for geneSets ( a series of histograms). For generic histograms, use hep.aida.

Version:

$Id: Histogram.java,v 1.3 2010/04/21 06:28:54 paul Exp $

Author:

Shahmil Merchant, Paul Pavlidis

Field Summary

Fields

Modifier and Type	Field and Description
protected static org.apache.commons.logging.Log	log

Constructor Summary

Constructors

Constructor and Description
Histogram(int numGeneSetSizes, int minGeneSetSize, int numRuns, double max, double min)

Method Summary

Methods

Modifier and Type	Method and Description
void	addExactNormalProbabilityComputer(int i, double mean, double variance)
void	calcNumOfBins()
double[]	getBins()
double	getBinSize()
int	getClassIndex(int geneSetSize, int minGeneSetSize)
double	getHistMax()
double	getHistMin()
double[]	getHistogram(int geneSetSize)
int	getMinGeneSetSize()
int	getNumBins()
int	getNumHistograms()
int	getNumRuns()
double	getProbability(int classSize, int binnum, boolean upperTail)
double	getValue(int geneSetSize, double rawscore, boolean upperTail)
void	print(Writer s) Prints the histogram to stdout.
void	setNumRuns(int runs)
void	tocdf() Convert raw histograms to CDFs.
String	toString()
void	update(int classSize, double value) Update the count for one bin.

Methods inherited from class java.lang.Object

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

Field Detail

log

protected static final org.apache.commons.logging.Log log

Constructor Detail

Histogram

public Histogram(int numGeneSetSizes,
         int minGeneSetSize,
         int numRuns,
         double max,
         double min)

Parameters:

numGeneSets -

minGeneSetSize -

numRuns -

max -

min -

Method Detail

calcNumOfBins

public void calcNumOfBins()

setNumRuns

public void setNumRuns(int runs)

Parameters:

runs - int

update

public void update(int classSize,
          double value)

Update the count for one bin.

Parameters:

row - int

value - double

tocdf

public void tocdf()

Convert raw histograms to CDFs.

getBinSize

public double getBinSize()

Returns:

double

getHistMin

public double getHistMin()

Returns:

double

getHistMax

public double getHistMax()

Returns:

double

getNumBins

public int getNumBins()

Returns:

int

getNumHistograms

public int getNumHistograms()

getNumRuns

public int getNumRuns()

Returns:

int

getMinGeneSetSize

public int getMinGeneSetSize()

toString

public String toString()

Overrides:

toString in class Object

getClassIndex

public int getClassIndex(int geneSetSize,
                int minGeneSetSize)

Parameters:

class_size - int

min_class_size - int

Returns:

int

getValue

public double getValue(int geneSetSize,
              double rawscore,
              boolean upperTail)

Parameters:

geneSetSize - int - NOT the row, that is determined here.

rawscore - double

upperTail -

Returns:

double probability

getHistogram

public double[] getHistogram(int geneSetSize)

Parameters:

classSize -

Returns:

getBins

public double[] getBins()

Returns:

print

public void print(Writer s)
           throws IOException

Prints the histogram to stdout.

Throws:

IOException

getProbability

public double getProbability(int classSize,
                    int binnum,
                    boolean upperTail)

Parameters:

upperTail -

row - int

binnum - int

Returns:

double

addExactNormalProbabilityComputer

public void addExactNormalProbabilityComputer(int i,
                                     double mean,
                                     double variance)

Parameters:

i -

mean -

variance -