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