trans.cel
Class CelProcessor

java.lang.Object
  trans.cel.CelProcessor

public class CelProcessor

extends java.lang.Object

Application to process '.cela' files, wrapper for CelMapper, QuantileNormalization.

Constructor Summary

CelProcessor(java.lang.String[] args)

Method Summary

static boolean	anyNaNs(float[] ints) Looks for NaN in IntensityFeatures.
static boolean	anyNaNs(IntensityFeature[] ints) Looks for NaN in IntensityFeatures.
static void	breakAndSaveCelp(java.io.File celpFile, MapFeature[] features) Given a float[] celp file and the corresponding MapFeature[] will make a minimal
static void	breakSaveFeatureArray(java.util.ArrayList bpmapInfo, MapFeature[] mapFeatures, java.io.File celpFile) Use this method to break and save a celp float[] file into chromosomal components in a directory named after the celpFile minus the .celp extension.
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

Methods inherited from class java.lang.Object

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

Constructor Detail

CelProcessor

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

Method Detail

breakSaveFeatureArray

public static void breakSaveFeatureArray(java.util.ArrayList bpmapInfo,
                                         MapFeature[] mapFeatures,
                                         java.io.File celpFile)

Use this method to break and save a celp float[] file into chromosomal components in a directory named after the celpFile minus the .celp extension.

anyNaNs

public static boolean anyNaNs(IntensityFeature[] ints)

Looks for NaN in IntensityFeatures. Returns true if NaNs found, false if clean.

anyNaNs

public static boolean anyNaNs(float[] ints)

Looks for NaN in IntensityFeatures. Returns true if NaNs found, false if clean.

breakAndSaveCelp

public static void breakAndSaveCelp(java.io.File celpFile,
                                    MapFeature[] features)

Given a float[] celp file and the corresponding MapFeature[] will make a minimal

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)