All Classes
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All Classes Interface Summary Class Summary Enum Summary Exception Summary Class Description ByteMapper CalculatedSimilar Calculates the most similar sites to a site when needed (with a cache of the last site calculated)Correlation Abstract class for calculating LD.Data DataException Over arching exception for data related problemsDataType DoubleMapper EM Calculates LD using the expectation maximization methodFilterDefinition<D> FormatDefinition<D> InfoDefinition IntegerMapper<M> InvalidGenotypeException Exception to be thrown for an invalid genotypeKnni Class to perform standard kNNi imputationKnniLD Class to perform standard LD-kNNi imputationKnniLDOpt Wrapper around KnniLD to allow optimization of parametersKnniOpt Wrapper around Knni to allow optimization of parametersLinkImpute Main executable classMapper<M> Mask Represents a mask for calculating imputation accuracy.Meta Mode Class to perform Mode imputationNotEnoughGenotypesException Exception for when there aren't enough genotypes at a SNP to impute.Optimize Optimizes integer parameter values.Pearson Calculates LD as a simple Pearson correlationPhred PlinkNumeric Class for dealing with data in the plink .raw format.PlinkPed Class for dealing with data in the plink .ped format.Position Progress Interface for classes that show some sort of progress to standard outRepeatedSampleException Exception to be thrown if a sample name is repeatedRepeatedSNPException Exception to be thrown if a SNP name is repeatedSampleSnp Represents the position of a single genotype (i.e.SilentProgress A progress class that does nothing - i.e.Similar Interface for classes calculating most similar sites to a siteSortByIndexDouble Comparator to sort integer indicies based on the corresponding value in a double array.StoredSimilar Stores the sites most similar to a site for all sitesStringMapper TextProgress Draws and updates a progress bar to standard outTopQueue<E extends java.lang.Comparable<E>,V extends java.lang.Comparable<V>> Keeps track of the top n based on their assigned value.Value Interface representing something that is optimizable.VCF WrongNumberOfSNPsException Exception to be thrown if a sample has the wrong number of SNPs