R-Index

R

read(Options, T, Data) - Static method in interface pt.ist.phylolib.data.IReader: Reads data from an option of the given data type in the given options.
READ - Static variable in interface pt.ist.phylolib.data.IReader
reduce(Set<Edge>, Tree, Edge, Edge) - Method in class pt.ist.phylolib.command.optimization.LBR
reduce(Set<Edge>, Tree, Edge, Edge) - Method in class pt.ist.phylolib.command.optimization.Optimization: Reduces the given set of edges by removing the given edge and adds another given edge to the tree.
remove(Option) - Method in class pt.ist.phylolib.cli.Options: Returns the value and removes the association for the given Option.
remove(Edge) - Method in class pt.ist.phylolib.data.tree.Tree: Removes a given edge from this tree.
RepeatedCommandException - Exception in pt.ist.phylolib.exception: Represents an error derived from the definition of an unrepeatable command more than once in the command line arguments.
RepeatedCommandException(String) - Constructor for exception pt.ist.phylolib.exception.RepeatedCommandException
run(Arguments, Context, Command, ICommand.IGetter<T>, BiConsumer<Options, R>) - Static method in interface pt.ist.phylolib.command.ICommand: Runs the specified command with that input getter and output setter for the given arguments and context.

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