trans.misc
Class Util

java.lang.Object
  trans.misc.Util

public class Util

extends java.lang.Object

Static helper methods for all things Affy

Constructor Summary

Util()

Method Summary

static int	countNumberOfOligoPositions(int[][] startStops) Given an array of int[][start, stop] returns the total number of integers, stop included.
static float[][]	createVirtualCel(java.io.File celFile) Loads a text version cel file into a zeroed virtual chip.
static float[][]	createVirtualCel(java.lang.String[] lines) Loads a text version cel file into a zeroed virtual chip.
static float[]	fetchTextCelFileIntensities(java.io.File celFile) Fetches intensity values from a text version cel file.
static java.util.HashMap	getChromosomeNumber() Creates a HashMap of "chr1"=Byte(1) through "chr22"=Byte(22) plus chrX=23, chrY=24, and chrMT=25.
static java.lang.String[]	getNumberChromosome() Creates a String[] containing [1]"chr1", [2]"chr2" ...
static Sgr[]	loadGrFile(java.io.File grFile, java.lang.String chromName) Reads in an sgr file.
static Sgr[]	loadSgrFile(java.io.File sgrFile) Reads in an sgr file.
static void	main(java.lang.String[] args)
static double[]	minMaxWindowArray(Window[] win, int scoreIndex) Returns the min and max values of a given score index in a Window[].
static double[]	minMaxWindowScores(Window[] win, int scoreIndex) Finds min max score
static java.lang.String	parseChromosomeName(java.lang.String name) Attempts to parse a chromosome name.
static GrGraph	readSimpleGrBarFile(java.io.File simpleBarFile) This is a complete hack of Gregg Helt's IGB code to parse bar files.
static void	readTagValPairs(java.io.DataInput dis, int pair_count) Dummy method used for parsing binary stream.
static Window[]	removeLowOligoWindows(Window[] win, int minNumberOligos) Removes windows that contain < minNumberOligos.
static void	sortIntervalsBySubWindowMedianRatio(Interval[] intervals) Sorts an array of Interval by the median ratio of the best SubWindow.
static java.util.HashMap	splitIntervalArrayListByChromosome(java.util.ArrayList intervals) Splits an ArrayList containing Interval by chromosome into a HashMap.
static Window[][]	splitWindowsByChromosome(Window[] win)
static boolean	writeSimpleBarFile(GrGraph gr, java.io.File barFile) Writes a simple bar format graph for a xxx.gr type graph.
static boolean	writeSimpleBarFile(java.lang.String chromosome, java.lang.String genomeVersion, int[] basePositions, float[] intensityValues, java.io.File barFile) Writes a simple bar format graph for a xxx.gr type graph.

Methods inherited from class java.lang.Object

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

Constructor Detail

Util

public Util()

Method Detail

main

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

sortIntervalsBySubWindowMedianRatio

public static void sortIntervalsBySubWindowMedianRatio(Interval[] intervals)

Sorts an array of Interval by the median ratio of the best SubWindow. If a sub is not found then the score is set to zero. Modifies the original array. Sets the sortBy field to the median ratio score.

splitIntervalArrayListByChromosome

public static java.util.HashMap splitIntervalArrayListByChromosome(java.util.ArrayList intervals)

Splits an ArrayList containing Interval by chromosome into a HashMap.

minMaxWindowScores

public static double[] minMaxWindowScores(Window[] win,
                                          int scoreIndex)

Finds min max score

readSimpleGrBarFile

public static GrGraph readSimpleGrBarFile(java.io.File simpleBarFile)

This is a complete hack of Gregg Helt's IGB code to parse bar files. It only works on single graph xxx.gr type files, ie two columns, ints and floats. Is compatable with TiMAT's Gr2Bar writer.

readTagValPairs

public static void readTagValPairs(java.io.DataInput dis,
                                   int pair_count)
                            throws java.io.IOException

Dummy method used for parsing binary stream.

Throws:

java.io.IOException

writeSimpleBarFile

public static boolean writeSimpleBarFile(GrGraph gr,
                                         java.io.File barFile)

Writes a simple bar format graph for a xxx.gr type graph. Modified from IGB code.

writeSimpleBarFile

public static boolean writeSimpleBarFile(java.lang.String chromosome,
                                         java.lang.String genomeVersion,
                                         int[] basePositions,
                                         float[] intensityValues,
                                         java.io.File barFile)

Writes a simple bar format graph for a xxx.gr type graph. Modified from IGB code.

parseChromosomeName

public static java.lang.String parseChromosomeName(java.lang.String name)

Attempts to parse a chromosome name. Returns null if it fails. Looks for chr1-22, chrX, chrY, chrM, and chrMT.

getChromosomeNumber

public static java.util.HashMap getChromosomeNumber()

Creates a HashMap of "chr1"=Byte(1) through "chr22"=Byte(22) plus chrX=23, chrY=24, and chrMT=25.

getNumberChromosome

public static java.lang.String[] getNumberChromosome()

Creates a String[] containing [1]"chr1", [2]"chr2" ... [23]"chrX", [24]"chrY", [25]"chrM", [26]"chrM", [27]"chrMT", and [28]"chrCtrls". [0] is empty.

minMaxWindowArray

public static double[] minMaxWindowArray(Window[] win,
                                         int scoreIndex)

Returns the min and max values of a given score index in a Window[].

Returns:

double[]{min, max}

removeLowOligoWindows

public static Window[] removeLowOligoWindows(Window[] win,
                                             int minNumberOligos)

Removes windows that contain < minNumberOligos.

loadSgrFile

public static Sgr[] loadSgrFile(java.io.File sgrFile)

Reads in an sgr file.

loadGrFile

public static Sgr[] loadGrFile(java.io.File grFile,
                               java.lang.String chromName)

Reads in an sgr file.

fetchTextCelFileIntensities

public static float[] fetchTextCelFileIntensities(java.io.File celFile)

Fetches intensity values from a text version cel file.

createVirtualCel

public static float[][] createVirtualCel(java.io.File celFile)

Loads a text version cel file into a zeroed virtual chip.

createVirtualCel

public static float[][] createVirtualCel(java.lang.String[] lines)

Loads a text version cel file into a zeroed virtual chip.

countNumberOfOligoPositions

public static int countNumberOfOligoPositions(int[][] startStops)

Given an array of int[][start, stop] returns the total number of integers, stop included.

splitWindowsByChromosome

public static Window[][] splitWindowsByChromosome(Window[] win)