Uses of Class
State

Uses of State in <Unnamed>

Fields in <Unnamed> declared as State

(package private) State

Exon.state

Fields in <Unnamed> with type parameters of type State

(package private) static java.util.HashMap<java.lang.String,State>	HiddenMarkovModel.States
(package private) static java.util.HashMap<State,java.util.HashMap<State,java.lang.Double>>	State.transitionProbabilities
(package private) static java.util.HashMap<State,java.util.HashMap<State,java.lang.Double>>	State.transitionProbabilities

Methods in <Unnamed> that return State

private static State

HiddenMarkovModel.getStateFromIndex(int stateIndex) From state number, figures out the state

Methods in <Unnamed> that return types with arguments of type State

private static java.util.ArrayList<java.util.HashMap<State,java.lang.Double>>	HiddenMarkovModel.computeBackwardProbabilities(java.util.ArrayList<Exon> exons, java.util.ArrayList<Exon> expectedValues, java.util.ArrayList<Exon> stdDeviations, int nSamples, cern.jet.random.Gamma gamma, double gammaK, double gammaTheta, double gammaSNPsK, double gammaSNPsTheta) Computes the backward probabilities for the observation
private static java.util.ArrayList<java.util.HashMap<State,java.lang.Double>>	HiddenMarkovModel.computeForwardProbabilities(java.util.ArrayList<Exon> exons, java.util.ArrayList<Exon> expectedValues, java.util.ArrayList<Exon> stdDeviations, int nSamples, cern.jet.random.Gamma gamma, double gammaK, double gammaTheta, double gammaSNPsK, double gammaSNPsTheta) Computes the forward probabilities for the observation
static java.util.HashMap<java.lang.String,State>	State.initializeStates(java.lang.String parameterFile) Initializes all the states with the values in the parameter file

Methods in <Unnamed> with parameters of type State

static double	State.getEmissionProbability(double observedFPKM, double observedSNPs, double expectedFPKM, double expectedSNPs, double stdDevFPKM, double stdDevSNPs, double normalizationFPKM, double normalizationSNPs, State s) To remove
static java.lang.Double	State.getEmissionProbability(Exon exon, Exon expected, Exon stdDev, State s) To remove
static double	State.getLogEmissionProbability(Exon exon, Exon expected, Exon stdDev, State s, int nSamples, cern.jet.random.Gamma gamma, double gammaK, double gammaTheta, double gammaSNPsK, double gammaSNPsTheta) Calculates the emission probability for the observation at a particular exon, in state s
static double	State.getTransitionProbability(State s1, State s2, int lengthOfIntron, int lengthOfExon) Gets the transition probability from state s1 -> state s2