trans.roc
Class ParsePatternedWindows

java.lang.Object
  trans.roc.ParsePatternedWindows

public class ParsePatternedWindows

extends java.lang.Object

Finds RocWindows upstream and withing the neighborhood of the ATG start site of a patterned gene list.

Constructor Summary

ParsePatternedWindows(java.lang.String[] args)

Method Summary

static GeneGroup[]	extractGeneGroups(java.util.HashMap geneGroups, java.lang.String[] geneList) Pulls out a sub set of GeneGroups with the names in the geneList.
static RocWindow[]	fetchProximalWindows(GeneGroup[] geneGrps, RocWindow[] windows, int sizeUpstream)
static RocWindow[]	filterRocWindows(RocWindow[] windows, double cutOff, boolean greaterThan) Scans an array of RocWindow for those that are greater than (or less than if boolean is false) or equal to the cutOff.
static RocWindow[]	loadRocWindows(java.io.File[] arrayLists) Loads all the RocWindows into one from serialized ArrayLists of RocWindows.
static RocWindow[]	loadTxtRocFile(java.io.File file) reads a txt roc window (chrom, start, stop, middle(not used), score).
static void	main(java.lang.String[] args)
static void	printChroms(RocWindow[] r)
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles
static void	writeSGRFile(RocWindow[] r, java.io.File file) Writes an sgr file.
static void	writeTxtRocFile(RocWindow[] r, java.io.File file) Writes a chrom, start, stop, score file.

Methods inherited from class java.lang.Object

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

Constructor Detail

ParsePatternedWindows

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

Method Detail

writeSGRFile

public static void writeSGRFile(RocWindow[] r,
                                java.io.File file)

Writes an sgr file.

writeTxtRocFile

public static void writeTxtRocFile(RocWindow[] r,
                                   java.io.File file)

Writes a chrom, start, stop, score file.

loadTxtRocFile

public static RocWindow[] loadTxtRocFile(java.io.File file)

reads a txt roc window (chrom, start, stop, middle(not used), score).

printChroms

public static void printChroms(RocWindow[] r)

filterRocWindows

public static RocWindow[] filterRocWindows(RocWindow[] windows,
                                           double cutOff,
                                           boolean greaterThan)

Scans an array of RocWindow for those that are greater than (or less than if boolean is false) or equal to the cutOff. Returns those that pass.

loadRocWindows

public static RocWindow[] loadRocWindows(java.io.File[] arrayLists)

Loads all the RocWindows into one from serialized ArrayLists of RocWindows.

extractGeneGroups

public static GeneGroup[] extractGeneGroups(java.util.HashMap geneGroups,
                                            java.lang.String[] geneList)

Pulls out a sub set of GeneGroups with the names in the geneList.

fetchProximalWindows

public static RocWindow[] fetchProximalWindows(GeneGroup[] geneGrps,
                                               RocWindow[] windows,
                                               int sizeUpstream)

printDocs

public static void printDocs()

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign new varibles

main

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