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

G

getArray() - Method in class Mask.Mask
Returns an array of masked genotypes (true = masked, false = unmasked).
getArray(int, int) - Method in interface Files.VCFMappers.Mapper
 
getBestParameter() - Method in class Utils.Optimize
Returns the optimized parameters
getBestValue() - Method in class Utils.Optimize
Returns the optimized value
getChrom() - Method in class Files.VCFData.Position
 
getData() - Method in class Files.VCF
 
getFormat() - Method in class Files.VCFData.Position
 
getFormatDefintion(String) - Method in class Files.VCFData.Meta
 
getID() - Method in class Files.VCFData.FilterDefinition
 
getID() - Method in class Files.VCFData.FormatDefinition
 
getID() - Method in class Files.VCFData.InfoDefinition
 
getInfoDefinitions() - Method in class Files.VCFData.Meta
 
getInfoDefintion(String) - Method in class Files.VCFData.Meta
 
getList() - Method in class Utils.TopQueue
Returns the entries in the queue as an ordered list
getList(int) - Method in class Utils.TopQueue
Returns the entries in the queue as an ordered list.
getMap() - Method in class Utils.TopQueue
Get a (unsorted) map of entries and their values.
getMeta() - Method in class Files.VCF
 
getMeta(String) - Method in class Files.PlinkNumeric
Returns the meta data associated with a sample
getMeta(String) - Method in class Files.PlinkPed
Returns the meta data associated with a sample
getMetaHead() - Method in class Files.PlinkNumeric
Returns the meta header data - i.e.
getPosition() - Method in class Files.VCFData.Position
 
getPosition(String, String) - Method in class Files.VCFData.Data
 
getPositions() - Method in class Files.VCFData.Data
 
getSample() - Method in class Mask.SampleSnp
Get the sample
getSamples() - Method in class Files.PlinkNumeric
Returns the samples associated with this Plink object
getSamples() - Method in class Files.PlinkPed
Returns the samples associated with this Plink object
getSamples() - Method in class Files.VCFData.Data
 
getSet() - Method in class Mask.Mask
Returns a list of masked genotypes.
getSimilar(int) - Method in class Similarity.CalculatedSimilar
 
getSimilar(int) - Method in interface Similarity.Similar
Get an array of most similar sites for the given site
getSimilar(int) - Method in class Similarity.StoredSimilar
 
getSnp() - Method in class Mask.SampleSnp
Get the SNP
getSNPs() - Method in class Files.PlinkNumeric
Returns the SNPs associated with this Plink object
getValue(Position, int, FormatDefinition) - Method in class Files.VCFData.Data
 
getValue(Position, String, FormatDefinition) - Method in class Files.VCFData.Data
 
A B C D E F G H I K L M N O P R S T U V W 
All Classes All Packages