- Range - Class in Utils
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Used to represent a range (using doubkes)
- Range(double, double) - Constructor for class Utils.Range
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Constructor.
- rank(double[]) - Static method in class Utils.Array1D
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Returns the rank of each element in an array.
- RateCategory - Class in Models
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Represents a rate category of a phylogenetic model.
- RateCategory(String[][], RateCategory.FrequencyType, HashMap<String, Integer>) - Constructor for class Models.RateCategory
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Constrcutor for when the root distribution is defined as the stationary
or quasi-staionary distribution.
- RateCategory(String[][], String[], HashMap<String, Integer>) - Constructor for class Models.RateCategory
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Constructor for when the root distribution is defined.
- RateCategory.FrequencyType - Enum in Models
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Enumeration of the different ways of defining the root frequency
- RateCategory.RateException - Exception in Models
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Exception thrown if there is a problem within a RateClass
- RateCategory.RateException(String, String, String, Throwable) - Constructor for exception Models.RateCategory.RateException
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Constructor when there is a problem at a specific point in the rate matrix
or frequency array
- RateCategory.RateException(String) - Constructor for exception Models.RateCategory.RateException
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Constructor for other exception when there isn't an underlying cause
- RateCategory.RateException(String, Throwable) - Constructor for exception Models.RateCategory.RateException
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Constructor for other exception when there is an underlying cause
- rates(double, int) - Static method in class Maths.Gamma
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Returns the rates that should be used for a set number of rate categories
and a set value of alpha as per the methodology of Yang 1993
- readLine() - Method in class Utils.CommentedFileReader
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Reads a line from the file
- recalculateMatrix() - Method in class Parameters.Parameters
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Tests whether any parameters that would require recalculation of the
probability matrices have been changed since the last call to
Parameters.calculated()
- recode(Map<String, String>) - Method in class Alignments.Alignment
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Recodes the alignment and returns it
- recode(Map<String, String>) - Method in class Alignments.Site
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Recodes the site and returns it
- reset() - Method in class Utils.TimePassed
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Reset the timer.
- restart(Calculator, File) - Method in class Optimizers.GoldenSection
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- restart(Calculator, File, File) - Method in class Optimizers.GoldenSection
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- restart(Calculator, File) - Method in class Optimizers.NelderMead
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- restart(Calculator, File, File) - Method in class Optimizers.NelderMead
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- restart(Calculator, File) - Method in interface Optimizers.Optimizer
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- restart(Calculator, File, File) - Method in interface Optimizers.Optimizer
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- reverseLookup(Map<K, V>, V) - Static method in class Utils.MapUtils
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Reverse lookup in the map.
- reverseLookupMulti(Map<K, V>, V) - Static method in class Utils.MapUtils
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Reverse lookup in the map.
- run() - Method in class Likelihood.Calculator.SiteCalculator
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