net.maizegenetics.analysis.imputation

Class TransitionProbability

net.maizegenetics.analysis.imputation.TransitionProbability

Direct Known Subclasses:

TransitionProbabilityWithVariableRecombination

public class TransitionProbability

Field Detail

probabilityOfATransition

protected kotlin.Array[] probabilityOfATransition

adjustedProbability

protected kotlin.Array[] adjustedProbability

positions

protected kotlin.Array[] positions

avgSegmentLength

protected double avgSegmentLength

Method Detail

setTransitionProbability

public void setTransitionProbability(kotlin.Array[] probabilityMatrix)

Use this function to set the transition probability matrix when it is to be used without specifying nodes for getTransitionProbability

Parameters:

probabilityMatrix - the matrix of transition probabilities, rows = state1, columns = state2

getTransitionProbability

public double getTransitionProbability(int state1,
                                       int state2)

getLnTransitionProbability

public double getLnTransitionProbability(int state1,
                                         int state2)

getNumberOfStates

public int getNumberOfStates()

setTransitionCounts

public void setTransitionCounts(kotlin.Array[] transitionCounts,
                                int chromosomeLength,
                                int numberOfTaxa)

Parameters:

transitionCounts - the transition counts for this set of

chromosomeLength -

numberOfTaxa -

setNode

public void setNode(int node)

setAverageSegmentLength

public void setAverageSegmentLength(double length)

setPositions

public void setPositions(kotlin.Array[] positions)