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

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indexAt(int) - Method in class jbil.sequence.ByteArraySequence

indexAt(int) - Method in class jbil.sequence.Sequence

Gets the position in the base alphabet of the symbol at a given position in the sequence.

indexOf(Object) - Method in class jbil.sequence.Alphabet

Gets the position of a given symbol object in the alphabet.

INPUT_ALPHABET - Static variable in class jbil.sequence.GibbsMotifSiteSampler

INPUT_SEQUENCES - Static variable in class jbil.sequence.GibbsMotifSiteSampler

insert(int, Symbol) - Method in class jbil.sequence.ByteArraySequence

insert(int, Sequence) - Method in class jbil.sequence.ByteArraySequence

insert(int, Symbol) - Method in class jbil.sequence.Sequence

Inserts a new symbol at a given position in this sequence.

insert(int, Sequence) - Method in class jbil.sequence.Sequence

Inserts a sequence at a given position in this sequence.

insert(int, Symbol) - Method in class jbil.sequence.SymbolArraySequence

insert(int, Sequence) - Method in class jbil.sequence.SymbolArraySequence

intersection(Alphabet) - Method in class jbil.sequence.Alphabet

Computes the intersection between this alphabet and a given alphabet.

intersection(char[], char[]) - Static method in class jbil.util.ArrayUtilities

Computes the intersection between two char arrays.

IntIntervalDist - Class in jbil.rv

Distribution for an integer-valued r.v.

IntIntervalDist(int, double[]) - Constructor for class jbil.rv.IntIntervalDist

Creates a distribution for an integer-valued r.v.

IntIntervalGen - Class in jbil.rv

Random number generator for the

IntIntervalGen(RandomStream, IntIntervalDist) - Constructor for class jbil.rv.IntIntervalGen

InvalidSymbolException - Exception in jbil.sequence

Runtime exception typically used to indicate problems in sequence operations involving invalid symbols, e.g.

InvalidSymbolException() - Constructor for exception jbil.sequence.InvalidSymbolException

Creates a new invalid symbol exception.

InvalidSymbolException(String) - Constructor for exception jbil.sequence.InvalidSymbolException

Creates a new invalid symbol exception with an associated message.

invert() - Method in class jbil.common.Pair

Creates a new pair with the same elements of this pair in inversed order.

invert(boolean[]) - Static method in class jbil.util.BooleanArrayUtilities

Inverts a boolean array.

isActiveTrie(int) - Method in class jbil.sequence.TrieForest

Checks whether the trie at a given position is active or not.

isAtomic() - Method in class jbil.sequence.AtomicCharSymbol

isAtomic() - Method in class jbil.sequence.HighOrderCharSymbol

isAtomic() - Method in interface jbil.sequence.Symbol

isLocked() - Method in class jbil.sequence.Alphabet