trans.tpmap
Class MapSplitter

java.lang.Object
  trans.tpmap.MapSplitter

public class MapSplitter

extends java.lang.Object

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

Constructor Summary

MapSplitter(MapFeature[] features, java.io.File saveDirectory)
For running in combination with BPMapProcessor

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()
void	splitTPMap()

Methods inherited from class java.lang.Object

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

Constructor Detail

MapSplitter

public MapSplitter(MapFeature[] features,
                   java.io.File saveDirectory)

For running in combination with BPMapProcessor

Method Detail

splitTPMap

public void splitTPMap()

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 TPMapSplitter on a .tpmap file.

gatherInfo

public void gatherInfo()