/// <summary>
/// Constructor
/// </summary>
/// <param name="data"></param>
/// <param name="mixturesDistribution"></param>
/// <param name="haploidMeans"></param>
public HiddenMarkovModel(List <List <double> > data, List <MultivariateNegativeBinomial> mixturesDistribution, List <double> haploidMeans)
{
// HMM set-up
nStates = mixturesDistribution.Count;
length = data.Count;
_stateProbabilities = new double[nStates];
_emission = new NegativeBinomialMixture(mixturesDistribution, haploidMeans);
_variances = mixturesDistribution.Select(x => x.Variances).ToList();
_transition = CanvasCommon.Utilities.MatrixCreate(nStates, nStates);
for (int i = 0; i < nStates; i++)
{
for (int j = 0; j < nStates; j++)
{
if (i == j)
{
_transition[i][j] = selfTransition;
}
else
{
_transition[i][j] = (1.0 - selfTransition) / (nStates - 1);
}
}
}
// alpha-beta algorithm
_beta = CanvasCommon.Utilities.MatrixCreate(length, nStates);
_alpha = CanvasCommon.Utilities.MatrixCreate(length, nStates);
// marginal posterior distibution
_gamma = CanvasCommon.Utilities.MatrixCreate(nStates, length);
// joint posterior distibution
_epsilon = CanvasCommon.Utilities.MatrixCreate(length, nStates, nStates);
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="data"></param>
/// <param name="mixturesDistribution"></param>
/// <param name="haploidMeans"></param>
public HiddenMarkovModel(List <List <double> > data, List <MultivariateNegativeBinomial> mixturesDistribution, List <double> haploidMeans, bool isPerSample)
{
// HMM set-up
nStates = mixturesDistribution.Count;
length = data.Count;
_stateProbabilities = new double[nStates];
_emission = new NegativeBinomialMixture(mixturesDistribution, haploidMeans, isPerSample);
_transition = CanvasCommon.Utilities.MatrixCreate(nStates, nStates);
for (int i = 0; i < nStates; i++)
{
for (int j = 0; j < nStates; j++)
{
if (i == j)
{
_transition[i][j] = selfTransition;
}
else
{
_transition[i][j] = (1.0 - selfTransition) / (nStates - 1);
}
}
_stateProbabilities[i] = 1f / nStates;
}
// alpha-beta algorithm
CanvasCommon.Utilities.MatrixCreate(length, nStates);
CanvasCommon.Utilities.MatrixCreate(length, nStates);
// marginal posterior distibution
CanvasCommon.Utilities.MatrixCreate(nStates, length);
// joint posterior distibution
CanvasCommon.Utilities.MatrixCreate(length, nStates, nStates);
}
