nix.affy.main
Class CelMapper

java.lang.Object
  nix.affy.main.CelMapper

public class CelMapper

extends java.lang.Object

Substitutes coordinates in a bpmap file for actual intensity values from a .cel file. Will write the .celInt pseudo bpmap file to disk.

Constructor Summary

CelMapper(int rows, java.lang.String bpmapFile, int numLinesInbpmapFile, BPMapFeature[][] duplicateFeatures, boolean useMMData, boolean printStats)
For use with the CelProcessor

CelMapper(java.lang.String[] args)
For stand alone use to create a text output file.

Method Summary

static void	averageDuplicates(BPMapFeature[][] dups, float[][] intensities) Averages the intesities of duplicates, will not include 0 values in average.
static double[]	fetchNonMappedIntensities(float[][] intensities, boolean[][] mapped) Sums the values of a float[][] array provided the matching boolean is false.
static void	main(java.lang.String[] args)
void	mapCelFiles(java.lang.String[] files)
static void	printDocs()
void	printMapCelFiles(java.io.File bpmapFile) Method for maping a cel file to a bpmap method and printing a tab delimited text file.
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles
static float[][]	zeroedFloatArray(int x, int y) Makes a float[x][y] and fills it with zeros.

Methods inherited from class java.lang.Object

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

Constructor Detail

CelMapper

public CelMapper(int rows,
                 java.lang.String bpmapFile,
                 int numLinesInbpmapFile,
                 BPMapFeature[][] duplicateFeatures,
                 boolean useMMData,
                 boolean printStats)

For use with the CelProcessor

CelMapper

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

For stand alone use to create a text output file.

Method Detail

printMapCelFiles

public void printMapCelFiles(java.io.File bpmapFile)

Method for maping a cel file to a bpmap method and printing a tab delimited text file. Replaces coordinates with intensity value thus: Seq, num1BPMisMatches or Affys t/f, chrom, startPos, PMIntensity, MMIntensity

mapCelFiles

public void mapCelFiles(java.lang.String[] files)

fetchNonMappedIntensities

public static double[] fetchNonMappedIntensities(float[][] intensities,
                                                 boolean[][] mapped)

Sums the values of a float[][] array provided the matching boolean is false. Assumes all arrays are the same size. Returns the number of non mappers and the sum of their values.

zeroedFloatArray

public static float[][] zeroedFloatArray(int x,
                                         int y)

Makes a float[x][y] and fills it with zeros.

averageDuplicates

public static void averageDuplicates(BPMapFeature[][] dups,
                                     float[][] intensities)

Averages the intesities of duplicates, will not include 0 values in average. This is used by CelMapper.

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 any new varibles

printDocs

public static void printDocs()