trans.roc
Class ParsePatternedWindows

java.lang.Object
  extended bytrans.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)