trans.qc
Class Parser1lq

java.lang.Object
  trans.qc.Parser1lq

public class Parser1lq

extends java.lang.Object

Extracts control an pm lines from a text 1lq file. A serialized int[][][] for the xy coordinates is saved.

Constructor Summary

Parser1lq(java.lang.String[] args)

Method Summary

static int[]	countNumberIntensities(int[][][] coordinates) Calculate number of noSynth, dim, bright controls, and pm probes.
static int[][][]	extract1lqFile(java.io.File onelqFile, java.io.File outputFile) Fetches coordinates for DESTYPEs of 0, 3, -3, 6, or -6 (Control) and PM -111, 111.
void	extract1lqFiles() Extracts control oligo information from 1lq files.
static void	main(java.lang.String[] args)
static float[][]	makeVirtualCel(int[][] xyCoor, int numRows) Make a virtual cel file loading xyCoors with an intensity of 100.
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

Parser1lq

public Parser1lq(java.lang.String[] args)

Method Detail

extract1lqFile

public static int[][][] extract1lqFile(java.io.File onelqFile,
                                       java.io.File outputFile)

Fetches coordinates for DESTYPEs of 0, 3, -3, 6, or -6 (Control) and PM -111, 111. Lumps sense and antisense together -6/6, -3/-3, -111/111 int[probe index][x,y] order noSynth, dim, bright, and pm. Returns null if a problem is encountered.

extract1lqFiles

public void extract1lqFiles()

Extracts control oligo information from 1lq files.

makeVirtualCel

public static float[][] makeVirtualCel(int[][] xyCoor,
                                       int numRows)

Make a virtual cel file loading xyCoors with an intensity of 100.

countNumberIntensities

public static int[] countNumberIntensities(int[][][] coordinates)

Calculate number of noSynth, dim, bright controls, and pm probes.

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 any new varibles

printDocs

public static void printDocs()