trans.cel
Class MakeChromosomeSets

java.lang.Object
  trans.cel.MakeChromosomeSets

public class MakeChromosomeSets

extends java.lang.Object

Constructor Summary

MakeChromosomeSets(java.lang.String[] args)

Method Summary

static IntensityFeature[]	collapseIntensityFeatureArray(IntensityFeature[][] fs) Collapses an uneven array of IntensityFeature[][] to IntensityFeature[].
static java.io.File[]	fetchChromosomeFiles(java.io.File[] chipDir, java.lang.String chromosomeName) Extracts all the Files with a given chromosome name from a list of directories
static IntensityFeature[]	fetchIntensityFeatures(java.io.File[] f) Loads IntensityFeature[]s into a single master.
static void	main(java.lang.String[] args)
long	makeSets(java.io.File[] chipSetDirectories, java.io.File saveDirectory) Merges chromosome info together and saves as whole chromosomes, will also save the oligoPositions if oligoPositionsDirectory isn't null.
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles
static void	splitAndSaveIntensities(IntensityFeature[] ints, java.io.File f) Saves the intensities to file as a int[]
static void	splitAndSavePositions(IntensityFeature[] ints, java.io.File f) Saves the positions to file as a int[]

Methods inherited from class java.lang.Object

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

Constructor Detail

MakeChromosomeSets

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

Method Detail

makeSets

public long makeSets(java.io.File[] chipSetDirectories,
                     java.io.File saveDirectory)

Merges chromosome info together and saves as whole chromosomes, will also save the oligoPositions if oligoPositionsDirectory isn't null. Returns the total number of oligos found across all chromosomes.

splitAndSaveIntensities

public static void splitAndSaveIntensities(IntensityFeature[] ints,
                                           java.io.File f)

Saves the intensities to file as a int[]

splitAndSavePositions

public static void splitAndSavePositions(IntensityFeature[] ints,
                                         java.io.File f)

Saves the positions to file as a int[]

fetchIntensityFeatures

public static IntensityFeature[] fetchIntensityFeatures(java.io.File[] f)

Loads IntensityFeature[]s into a single master.

collapseIntensityFeatureArray

public static IntensityFeature[] collapseIntensityFeatureArray(IntensityFeature[][] fs)

Collapses an uneven array of IntensityFeature[][] to IntensityFeature[].

fetchChromosomeFiles

public static java.io.File[] fetchChromosomeFiles(java.io.File[] chipDir,
                                                  java.lang.String chromosomeName)

Extracts all the Files with a given chromosome name from a list of directories

processArgs

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

This method will process each argument and assign any new varibles

printDocs

public static void printDocs()

main

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