trans.tpmap
Class TPMapProcessor

java.lang.Object
  trans.tpmap.TPMapProcessor

public class TPMapProcessor

extends java.lang.Object

App for processing the tpmap file for use by downstream TiMAT applications.

Author:

nix

Constructor Summary

TPMapProcessor(java.lang.String[] args)

Method Summary

void	convertTPMapToFeatures(java.io.File tpmapFile) Converts a text tpmap to a MapFeature[] and tracks duplicates
java.util.ArrayList	filterChromosomeSpecificFeatures(java.util.ArrayList startsAL, java.util.ArrayList chromMapFeaturesAL)
void	filterMapFeatures()
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

TPMapProcessor

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

Method Detail

filterMapFeatures

public void filterMapFeatures()

filterChromosomeSpecificFeatures

public java.util.ArrayList filterChromosomeSpecificFeatures(java.util.ArrayList startsAL,
                                                            java.util.ArrayList chromMapFeaturesAL)

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)

convertTPMapToFeatures

public void convertTPMapToFeatures(java.io.File tpmapFile)

Converts a text tpmap to a MapFeature[] and tracks duplicates