util.bio.annotation
Class ExportIntergenicRegions

java.lang.Object
  util.bio.annotation.ExportIntergenicRegions

public class ExportIntergenicRegions

extends java.lang.Object

Constructor Summary

ExportIntergenicRegions(java.lang.String[] args)

Method Summary

void	exportIntergenicRegions()
static int[][]	fetchFalseBlocks(boolean[] b, int bpToTrim, int minSize)
static void	main(java.lang.String[] args)
boolean[]	maskBoolean(Gff3Feature[] features) Uses a boolean[] to score whether a base is part of an annotation (true) or not (false).
boolean	printBlocks(int[][] startStop, java.lang.String chromosome, java.io.File file) Prints a file containing the block regions.
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles

Methods inherited from class java.lang.Object

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

Constructor Detail

ExportIntergenicRegions

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

Method Detail

exportIntergenicRegions

public void exportIntergenicRegions()

printBlocks

public boolean printBlocks(int[][] startStop,
                           java.lang.String chromosome,
                           java.io.File file)

Prints a file containing the block regions. Strips off the extension from the file and appends the chromosome name.

fetchFalseBlocks

public static int[][] fetchFalseBlocks(boolean[] b,
                                       int bpToTrim,
                                       int minSize)

maskBoolean

public boolean[] maskBoolean(Gff3Feature[] features)

Uses a boolean[] to score whether a base is part of an annotation (true) or not (false).

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 new varibles

printDocs

public static void printDocs()