A B C D E F G H I K L M N O P R S T U V

G

GammaResult - Class in <Unnamed>

GammaResult(double, double) - Constructor for class GammaResult

geneName - Variable in class Exon

getEmissionProbability(double, double, double, double, double, double, double, double, State) - Static method in class State

To remove

getEmissionProbability(Exon, Exon, Exon, State) - Static method in class State

To remove

getFPKM(ArrayList<Expression>, ArrayList<Exon>) - Static method in class Exon

Given an array of exons and expression data, calculate the FPKM levels per exon

getGenomeWideGammaParametersK(ArrayList<Exon>) - Static method in class Exon

Find the k parameter for the Gamma distribution describing the genomewide coverage distribution MLE for Gamma

getGenomeWideGammaParametersSNPsK(ArrayList<Exon>) - Static method in class Exon

Find the k parameter for the Gamma distribution describing the genomewide heterozygosity distribution MLE for Gamma

getGenomeWideGammaParametersSNPsTheta(ArrayList<Exon>, double) - Static method in class Exon

Find the Theta parameter for the Gamma distribution describing the genomewide heterozygosity distribution MLE for Gamma

getGenomeWideGammaParametersTheta(ArrayList<Exon>, double) - Static method in class Exon

Find the Theta parameter for the Gamma distribution describing the genomewide coverage distribution MLE for Gamma

getLikelyValue(double, double) - Static method in class SimulateExonMeasurements

getLogEmissionProbability(Exon, Exon, Exon, State, int, Gamma, double, double, double, double) - Static method in class State

Calculates the emission probability for the observation at a particular exon, in state s

getNumberOfDifferences(String, String) - Static method in class Exon

Gets the number of differences (ie SNPs) between the two sequences

getReferenceSequence(RandomAccessFile) - Method in class Exon

Reads reference file and computes the reference sequence for the exon

getSNPs(ArrayList<Exon>, ArrayList<MappedReads>) - Static method in class Exon

Gets the number of SNPs per exon

getStateFromIndex(int) - Static method in class HiddenMarkovModel

From state number, figures out the state

getStateName() - Method in class State

For pretty-printing and for serving coffee with the code

getStates(ArrayList<Exon>, ArrayList<Exon>, ArrayList<Exon>, String, double, int, Gamma, double, double, double, double) - Static method in class HiddenMarkovModel

Gets the most likely states given the observations using forward-backward algorithm

getTransitionProbability(State, State, int, int) - Static method in class State

Gets the transition probability from state s1 -> state s2