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broad.core.motif.PositionWeightColumn Member List

This is the complete list of members for broad.core.motif.PositionWeightColumn, including all inherited members.

addPseudoCounts()broad.core.motif.PositionWeightColumn
computeProb()broad.core.motif.PositionWeightColumn
DEFAULT_ALPHABET_SIZEbroad.core.motif.PositionWeightColumnstatic
flatWeight(double infoTh)broad.core.motif.PositionWeightColumn
getAlphabetSize()broad.core.motif.PositionWeightColumn
getBaseIUB()broad.core.motif.PositionWeightColumn
getComplement()broad.core.motif.PositionWeightColumn
getInformationContent()broad.core.motif.PositionWeightColumn
getLogProb(char ch)broad.core.motif.PositionWeightColumn
getLogProb(int baseIdx)broad.core.motif.PositionWeightColumn
getLogRatio(char ch)broad.core.motif.PositionWeightColumn
getLogRatio(char i, boolean isNumSeq)broad.core.motif.PositionWeightColumn
getLogRatioWeightedByNegEntropy(char ch)broad.core.motif.PositionWeightColumn
getLogRatioWeightedByNegEntropy(char i, boolean isNumSeq)broad.core.motif.PositionWeightColumn
getProbability(int baseIndex)broad.core.motif.PositionWeightColumn
getWeight(int letterIndex)broad.core.motif.PositionWeightColumn
init(int alphabetSize)broad.core.motif.PositionWeightColumn
init()broad.core.motif.PositionWeightColumn
kullbackLeiber(PositionWeightColumn pwc)broad.core.motif.PositionWeightColumn
PositionWeightColumn()broad.core.motif.PositionWeightColumn
PositionWeightColumn(String[] rawData)broad.core.motif.PositionWeightColumn
PositionWeightColumn(int[] n)broad.core.motif.PositionWeightColumn
PositionWeightColumn(int nA, int nC, int nG, int nT)broad.core.motif.PositionWeightColumn
PositionWeightColumn(double[] freq)broad.core.motif.PositionWeightColumn
print()broad.core.motif.PositionWeightColumn
printProb()broad.core.motif.PositionWeightColumn
resetProbWithNullPriorProb()broad.core.motif.PositionWeightColumn
resetToUniformProb()broad.core.motif.PositionWeightColumn
setFromCounts(int[] n)broad.core.motif.PositionWeightColumnprotected
setNum(int[] n)broad.core.motif.PositionWeightColumn
setNum(int nA, int nC, int nG, int nT)broad.core.motif.PositionWeightColumn
toConsensus()broad.core.motif.PositionWeightColumn
toString()broad.core.motif.PositionWeightColumn
write(BufferedWriter bw, NumberFormat formatter)broad.core.motif.PositionWeightColumn