nix.affy.bpmap
Class MapSplitter

java.lang.Object
  nix.affy.bpmap.MapSplitter

public class MapSplitter

extends java.lang.Object

Splits a '.bpmap' text file into different chromosomes, helper script for BPMapProcessor.

Constructor Summary

MapSplitter(java.io.File bpmapFile, java.io.File saveDirectory, int numberBpmapDataLines)
For running in combination with BPMapProcessor

MapSplitter(java.lang.String fileName, int numberDataLines)
For running this alone.

Method Summary

static java.lang.String	breakSaveIntensityValues(java.util.ArrayList bpmapInfo, float[][] intensities, java.lang.String fullPathDir) Use this method to break a float[][] array into different float[][] by chromosome.
static java.lang.String	breakSaveIntensityValues(java.util.ArrayList bpmapInfo, float[] intensities, java.lang.String fullPathBaseName) Use this method to break a float[] array into different float[] by chromosome.
static java.lang.String	breakSaveIntensityValues(java.util.ArrayList bpmapInfo, int[][] intensities, java.lang.String fullPathDir) Use this method to break a int[][] array into different int[][] by chromosome.
static java.lang.String	breakSaveIntensityValues(java.util.ArrayList bpmapInfo, int[] intensities, java.lang.String fullPathBaseName) Use this method to break a int[] array into different int[] by chromosome.
void	breakSavePositions()
void	gatherInfo()
static void	main(java.lang.String[] args)
void	splitBPMap()

Methods inherited from class java.lang.Object

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

Constructor Detail

MapSplitter

public MapSplitter(java.lang.String fileName,
                   int numberDataLines)

For running this alone.

MapSplitter

public MapSplitter(java.io.File bpmapFile,
                   java.io.File saveDirectory,
                   int numberBpmapDataLines)

For running in combination with BPMapProcessor

Method Detail

splitBPMap

public void splitBPMap()

breakSavePositions

public void breakSavePositions()

breakSaveIntensityValues

public static java.lang.String breakSaveIntensityValues(java.util.ArrayList bpmapInfo,
                                                        int[] intensities,
                                                        java.lang.String fullPathBaseName)

Use this method to break a int[] array into different int[] by chromosome. Saves the int[] arrays to disk using the fullPathBaseName+ the chromosome name. bpmapInfo comes from running the BPMapSplitter on a .bpmap file.

breakSaveIntensityValues

public static java.lang.String breakSaveIntensityValues(java.util.ArrayList bpmapInfo,
                                                        float[] intensities,
                                                        java.lang.String fullPathBaseName)

Use this method to break a float[] array into different float[] by chromosome. Saves the float[] arrays to disk using the fullPathBaseName+ the chromosome name. bpmapInfo comes from running the BPMapSplitter on a .bpmap file.

breakSaveIntensityValues

public static java.lang.String breakSaveIntensityValues(java.util.ArrayList bpmapInfo,
                                                        int[][] intensities,
                                                        java.lang.String fullPathDir)

Use this method to break a int[][] array into different int[][] by chromosome. Saves the int[][] arrays to disk using the fullPathBaseName+ the chromosome name. bpmapInfo comes from running the BPMapSplitter on a .bpmap file.

breakSaveIntensityValues

public static java.lang.String breakSaveIntensityValues(java.util.ArrayList bpmapInfo,
                                                        float[][] intensities,
                                                        java.lang.String fullPathDir)

Use this method to break a float[][] array into different float[][] by chromosome. Saves the float[][] arrays to disk using the fullPathBaseName+ the chromosome name. bpmapInfo comes from running the BPMapSplitter on a .bpmap file.

gatherInfo

public void gatherInfo()

main

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