meme
Class MemeMotif

java.lang.Object
  meme.MemeMotif

public class MemeMotif

extends java.lang.Object

This contains info generated from parsing a meme report, each found motif is represented by this class.

Constructor Summary

MemeMotif()

Method Summary

double[][]	getAdd1PSPM()
int[][]	getFreqMatrix()
java.lang.String[]	getHits()
double[][]	getLLAdd1PSPM(double pA, double pC, double pG, double pT)
double[][]	getLLMemePSPM(double pA, double pC, double pG, double pT)
MemeParser	getMemeParser()
double[][]	getMemePSPM()
java.lang.String	getMotifDesc()
java.lang.String	getMotifSites()
java.lang.String	getMotifSumLn()
int	getNumberName()
static double[][]	makeAddOnePSPM(java.lang.String[] hits) This method returns a position specific probability weight matrix given an array of Strings, each of the same size, containing GATC, no gaps, no N's.
static int[][]	makeFrequencyMatrix(java.lang.String[] hits) Generates a matrix of the number of As Cc Gg Ts (top) by 1,2,3,4...positions in the motif (side) observed in all the Strings of the String[].
static double[][]	makeLLPSPM(double[][] PSPM, double pA, double pC, double pG, double pT) takes a double[][] where array[0] refers to the first position in a motif array[0][0 to 3] = probability of A, C, G, or T nucleotide at that position.
static double[][]	makePSPM(java.lang.String[] hits) This method returns a position specific probability weight matrix given an array of Strings, each of the same size, containing GATC, no gaps, no N's.
void	setHits(java.lang.String[] x)
void	setMemeParserRef(MemeParser x)
void	setMemePSPM(double[][] x)
void	setMotifDesc(java.lang.String x)
void	setMotifSites(java.lang.String x)
void	setMotifSumLn(java.lang.String x)
void	setNumberName(int x)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

MemeMotif

public MemeMotif()

Method Detail

getNumberName

public int getNumberName()

getMotifSumLn

public java.lang.String getMotifSumLn()

getMotifDesc

public java.lang.String getMotifDesc()

getMotifSites

public java.lang.String getMotifSites()

getHits

public java.lang.String[] getHits()

getMemePSPM

public double[][] getMemePSPM()

getLLMemePSPM

public double[][] getLLMemePSPM(double pA,
                                double pC,
                                double pG,
                                double pT)

getAdd1PSPM

public double[][] getAdd1PSPM()

getLLAdd1PSPM

public double[][] getLLAdd1PSPM(double pA,
                                double pC,
                                double pG,
                                double pT)

getMemeParser

public MemeParser getMemeParser()

setNumberName

public void setNumberName(int x)

setMotifSumLn

public void setMotifSumLn(java.lang.String x)

setMotifDesc

public void setMotifDesc(java.lang.String x)

setMotifSites

public void setMotifSites(java.lang.String x)

setHits

public void setHits(java.lang.String[] x)

setMemePSPM

public void setMemePSPM(double[][] x)

setMemeParserRef

public void setMemeParserRef(MemeParser x)

makeLLPSPM

public static double[][] makeLLPSPM(double[][] PSPM,
                                    double pA,
                                    double pC,
                                    double pG,
                                    double pT)

takes a double[][] where array[0] refers to the first position in a motif array[0][0 to 3] = probability of A, C, G, or T nucleotide at that position. MakeLLPSPM converts each nucleotide probablility to a log likelihood value by taking the natural log of the probability ration ie array[0][0]/ pA . pN is background probability of a particular nucleotide (ie 0.25)

toString

public java.lang.String toString()

makeAddOnePSPM

public static double[][] makeAddOnePSPM(java.lang.String[] hits)

This method returns a position specific probability weight matrix given an array of Strings, each of the same size, containing GATC, no gaps, no N's. The weight matrix is an Add One matrix where a single psuedo count is added to all base counts when a zero is found in a particular base bin. The order of the array is ACGT for each position in a single hit.

makePSPM

public static double[][] makePSPM(java.lang.String[] hits)

This method returns a position specific probability weight matrix given an array of Strings, each of the same size, containing GATC, no gaps, no N's. The order of the array is ACGT for each position in a single hit.

makeFrequencyMatrix

public static int[][] makeFrequencyMatrix(java.lang.String[] hits)

Generates a matrix of the number of As Cc Gg Ts (top) by 1,2,3,4...positions in the motif (side) observed in all the Strings of the String[]. The String[] should contain equal length Strings, comprised entirely of GATC.

getFreqMatrix

public int[][] getFreqMatrix()