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

R

r - Static variable in class jbil.sequence.ExtendedDNAAlphabet

The high order r={a,g} symbol

r() - Method in class jbil.sequence.ExtendedDNAAlphabet

RandomManager - Class in jbil.util

Singleton class that controls a system-wide RNG.

RandomUtilities - Class in jbil.util

Assorted Random utility functions.

RandomUtilities() - Constructor for class jbil.util.RandomUtilities

registerAlphabet(String, Alphabet) - Method in class jbil.sequence.AlphabetRegistry

Registers an alphabet, associating it to unique name.

remove(int) - Method in class jbil.sequence.Alphabet

Removes the symbol at a given position.

removeBaseSequence(Sequence) - Method in class jbil.sequence.FactorTrie

Removes one occurrence of a base sequence from the factor trie, that is, removes one occurrence of each factor of the appropriate length of this base sequence from the factor trie.

removeTrie(Trie) - Method in class jbil.sequence.TrieForest

Removes a trie from the forest.

reset() - Method in class jbil.sequence.Trie

Clears the trie.

resetNextSubstream() - Method in class jbil.util.JDKRandomStream

Unsupported operation

resetStartStream() - Method in class jbil.util.JDKRandomStream

Unsupported operation

resetStartSubstream() - Method in class jbil.util.JDKRandomStream

Unsupported operation

run() - Method in class jbil.common.AbstractAlgorithm

run() - Method in interface jbil.common.Algorithm

Executes the algorithm once.

run() - Method in class jbil.sequence.GibbsMotifSiteSampler