broad.core.motif.PositionWeightColumn Class Reference

Public Member Functions
	PositionWeightColumn ()
	PositionWeightColumn (String[] rawData)
	PositionWeightColumn (int[] n)
	PositionWeightColumn (int nA, int nC, int nG, int nT)
	PositionWeightColumn (double[] freq)
char	getBaseIUB ()
void	resetProbWithNullPriorProb ()
void	setNum (int[] n)
void	setNum (int nA, int nC, int nG, int nT)
PositionWeightColumn	getComplement ()
void	init (int alphabetSize)
void	init ()
double	getLogRatio (char ch)
double	getLogRatioWeightedByNegEntropy (char ch)
double	getLogProb (char ch)
double	getLogProb (int baseIdx)
double	getLogRatio (char i, boolean isNumSeq)
double	getLogRatioWeightedByNegEntropy (char i, boolean isNumSeq)
void	computeProb ()
void	printProb ()
void	print ()
char	toConsensus ()
double	getInformationContent ()
void	flatWeight (double infoTh)
void	resetToUniformProb ()
double	getWeight (int letterIndex)
void	write (BufferedWriter bw, NumberFormat formatter) throws IOException
String	toString ()
double	getProbability (int baseIndex)
int	getAlphabetSize ()
void	addPseudoCounts ()
double	kullbackLeiber (PositionWeightColumn pwc)

Static Public Attributes
static final int	DEFAULT_ALPHABET_SIZE = 4

Protected Member Functions
void	setFromCounts (int[] n)

Constructor & Destructor Documentation

broad.core.motif.PositionWeightColumn.PositionWeightColumn

(

)

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broad.core.motif.PositionWeightColumn.PositionWeightColumn

(

String[]

rawData

)

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broad.core.motif.PositionWeightColumn.PositionWeightColumn

(

int[]

n

)

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broad.core.motif.PositionWeightColumn.PositionWeightColumn	(	int	nA,
		int	nC,
		int	nG,
		int	nT
	)

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broad.core.motif.PositionWeightColumn.PositionWeightColumn

(

double[]

freq

)

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Member Function Documentation

void broad.core.motif.PositionWeightColumn.addPseudoCounts

(

)

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void broad.core.motif.PositionWeightColumn.computeProb

(

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void broad.core.motif.PositionWeightColumn.flatWeight

(

double

infoTh

)

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int broad.core.motif.PositionWeightColumn.getAlphabetSize

(

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char broad.core.motif.PositionWeightColumn.getBaseIUB

(

)

PositionWeightColumn broad.core.motif.PositionWeightColumn.getComplement

(

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double broad.core.motif.PositionWeightColumn.getInformationContent

(

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double broad.core.motif.PositionWeightColumn.getLogProb

(

char

ch

)

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double broad.core.motif.PositionWeightColumn.getLogProb

(

int

baseIdx

)

double broad.core.motif.PositionWeightColumn.getLogRatio

(

char

ch

)

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double broad.core.motif.PositionWeightColumn.getLogRatio	(	char	i,
		boolean	isNumSeq
	)

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double broad.core.motif.PositionWeightColumn.getLogRatioWeightedByNegEntropy

(

char

ch

)

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double broad.core.motif.PositionWeightColumn.getLogRatioWeightedByNegEntropy	(	char	i,
		boolean	isNumSeq
	)

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double broad.core.motif.PositionWeightColumn.getProbability

(

int

baseIndex

)

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double broad.core.motif.PositionWeightColumn.getWeight

(

int

letterIndex

)

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void broad.core.motif.PositionWeightColumn.init

(

int

alphabetSize

)

void broad.core.motif.PositionWeightColumn.init

(

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double broad.core.motif.PositionWeightColumn.kullbackLeiber

(

PositionWeightColumn

pwc

)

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void broad.core.motif.PositionWeightColumn.print

(

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void broad.core.motif.PositionWeightColumn.printProb

(

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void broad.core.motif.PositionWeightColumn.resetProbWithNullPriorProb

(

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void broad.core.motif.PositionWeightColumn.resetToUniformProb

(

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void broad.core.motif.PositionWeightColumn.setFromCounts ( int[]  n )

protected

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void broad.core.motif.PositionWeightColumn.setNum

(

int[]

n

)

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void broad.core.motif.PositionWeightColumn.setNum	(	int	nA,
		int	nC,
		int	nG,
		int	nT
	)

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char broad.core.motif.PositionWeightColumn.toConsensus

(

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String broad.core.motif.PositionWeightColumn.toString

(

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void broad.core.motif.PositionWeightColumn.write	(	BufferedWriter	bw,
		NumberFormat	formatter
	)		throws IOException

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Member Data Documentation

final int broad.core.motif.PositionWeightColumn.DEFAULT_ALPHABET_SIZE = 4

static

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The documentation for this class was generated from the following file:

• java/broad/core/motif/PositionWeightColumn.java