Uses of Class
Exon

Uses of Exon in <Unnamed>

Fields in <Unnamed> with type parameters of type Exon

(package private) static java.util.ArrayList<Exon>	SimulateExonMeasurements.exons
(package private) static java.util.ArrayList<Exon>	CreateExonFile.Exons
(package private) static java.util.ArrayList<Exon>	ConvertToExonFormat.Exons
(package private) static java.util.ArrayList<Exon>	CONDR.Exons
(package private) static java.util.ArrayList<Exon>	PileupToExon.Exons
(package private) static java.util.ArrayList<Exon>	CONDR.ExpectedValues
(package private) static java.util.ArrayList<Exon>	CONDR.StdDeviations

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

static java.util.ArrayList<Exon>	Exon.calculateExpectedValues(java.util.ArrayList<java.lang.String> baselineExonFileNames, int chromosome) Computes the expected value for each exon by average the values in the baseline files
static java.util.ArrayList<Exon>	Exon.calculateNormalizationFactor(java.util.ArrayList<java.lang.String> baselineExonFileNames, int i) Deprecated
static java.util.ArrayList<Exon>	Exon.calculateStdDevValues(java.util.ArrayList<java.lang.String> baselineExonFileNames, int chromosome, java.util.ArrayList<Exon> expectedValues) Computes the std deviation values for each exon by average the values in the baseline files
static java.util.ArrayList<Exon>	Exon.readAndStoreExonFile(java.lang.String exonFileName, int chromosome) Reads exon file; stores necessary info in array of exons
static java.util.ArrayList<Exon>	Exon.readExon(java.lang.String exonFileName, int chromosome) Parses the file (br) Reads file until the next chromosome Loads into an array of Exon objects

Methods in <Unnamed> with parameters of type Exon

private static void	Exon.calculateSNPPositions(Exon exon, MappedReads read) Calculated the positions of the SNPs
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

Method parameters in <Unnamed> with type arguments of type Exon

static java.util.ArrayList<Exon>	Exon.calculateStdDevValues(java.util.ArrayList<java.lang.String> baselineExonFileNames, int chromosome, java.util.ArrayList<Exon> expectedValues) Computes the std deviation values for each exon by average the values in the baseline files
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.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.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
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
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
(package private) static void	Exon.getFPKM(java.util.ArrayList<Expression> Expressions, java.util.ArrayList<Exon> Exons) Given an array of exons and expression data, calculate the FPKM levels per exon
static double	Exon.getGenomeWideGammaParametersK(java.util.ArrayList<Exon> exons) Find the k parameter for the Gamma distribution describing the genomewide coverage distribution MLE for Gamma
static double	Exon.getGenomeWideGammaParametersSNPsK(java.util.ArrayList<Exon> exons) Find the k parameter for the Gamma distribution describing the genomewide heterozygosity distribution MLE for Gamma
static double	Exon.getGenomeWideGammaParametersSNPsTheta(java.util.ArrayList<Exon> exons, double k) Find the Theta parameter for the Gamma distribution describing the genomewide heterozygosity distribution MLE for Gamma
static double	Exon.getGenomeWideGammaParametersTheta(java.util.ArrayList<Exon> exons, double k) Find the Theta parameter for the Gamma distribution describing the genomewide coverage distribution MLE for Gamma
static void	Exon.getSNPs(java.util.ArrayList<Exon> exons, java.util.ArrayList<MappedReads> mappedReads) Gets the number of SNPs per exon
static void	HiddenMarkovModel.getStates(java.util.ArrayList<Exon> exons, java.util.ArrayList<Exon> expectedValues, java.util.ArrayList<Exon> stdDeviations, java.lang.String parameterFileName, double threshold, int nSamples, cern.jet.random.Gamma gamma, double gammaK, double gammaTheta, double gammaSNPsK, double gammaSNPsTheta) Gets the most likely states given the observations using forward-backward algorithm
static void	HiddenMarkovModel.getStates(java.util.ArrayList<Exon> exons, java.util.ArrayList<Exon> expectedValues, java.util.ArrayList<Exon> stdDeviations, java.lang.String parameterFileName, double threshold, int nSamples, cern.jet.random.Gamma gamma, double gammaK, double gammaTheta, double gammaSNPsK, double gammaSNPsTheta) Gets the most likely states given the observations using forward-backward algorithm
static void	HiddenMarkovModel.getStates(java.util.ArrayList<Exon> exons, java.util.ArrayList<Exon> expectedValues, java.util.ArrayList<Exon> stdDeviations, java.lang.String parameterFileName, double threshold, int nSamples, cern.jet.random.Gamma gamma, double gammaK, double gammaTheta, double gammaSNPsK, double gammaSNPsTheta) Gets the most likely states given the observations using forward-backward algorithm
static void	Pileup.readData(java.util.ArrayList<Exon> exons, java.io.BufferedReader br) Reads the pileup and simultaneously updates the exon lists with appropriate values
private static int	SimulateExonMeasurements.SimulateRegion(java.util.ArrayList<Exon> ExpectedValues, java.util.ArrayList<Exon> StdDeviations, java.lang.String stateName, int index)
private static int	SimulateExonMeasurements.SimulateRegion(java.util.ArrayList<Exon> ExpectedValues, java.util.ArrayList<Exon> StdDeviations, java.lang.String stateName, int index)
(package private) static void	Exon.sortExons(java.util.ArrayList<Exon> data) Sort exons in order of their genomic position