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SampleSnp - Class in Mask
Represents the position of a single genotype (i.e.
SampleSnp(int, int) - Constructor for class Mask.SampleSnp
Default constructor
saveToFile(File) - Method in class Mask.Mask
Saves this mask to a file
setAddConstant(double) - Static method in class Methods.KnniLD
Sets the constant to add to avoid a distance of zero (since this causes problems later).
setSilent(boolean) - Static method in class Correlation.Correlation
Contols progress output to screen
setSilent(boolean) - Static method in class Methods.KnniLD
Contols progress output to screen
SilentProgress - Class in Utils
A progress class that does nothing - i.e.
SilentProgress() - Constructor for class Utils.SilentProgress
 
Similar - Interface in Similarity
Interface for classes calculating most similar sites to a site
Similarity - package Similarity
Provides classes for calculating similarity (based on LD) between SNPs.
sort() - Method in class Utils.SortByIndexDouble
Produce a sorted list of indicies for the entire array
SortByIndexDouble - Class in Utils
Comparator to sort integer indicies based on the corresponding value in a double array.
SortByIndexDouble(double[]) - Constructor for class Utils.SortByIndexDouble
Constructor.
SortByIndexDouble(double[], boolean) - Constructor for class Utils.SortByIndexDouble
Constructor.
StoredSimilar - Class in Similarity
Stores the sites most similar to a site for all sites
StoredSimilar(Map<Integer, List<Integer>>) - Constructor for class Similarity.StoredSimilar
Constructor
STRING - Files.VCFData.DataType
 
StringMapper - Interface in Files.VCFMappers
 
stripFormats() - Method in class Files.VCFData.Position
 
stripInfo() - Method in class Files.VCF
 
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