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

S

s - Static variable in class jbil.sequence.ExtendedDNAAlphabet

The high order s={g,c} symbol

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

sample(int) - Method in class jbil.sequence.AbstractFixedLengthSequenceModel

sample() - Method in interface jbil.sequence.FixedLengthSequenceModel

Samples a sequence with the apropriate length from this model.

sample() - Method in class jbil.sequence.MarkovFixedLengthSequenceModel

sample(int) - Method in interface jbil.sequence.SequenceModel

Samples a sequence from this model.

sample() - Method in class jbil.sequence.UniformFixedLengthSequenceModel

SAMPLE_SIZE - Static variable in class jbil.sequence.GibbsMotifSiteSampler

sampleN(int, int) - Method in class jbil.sequence.AbstractFixedLengthSequenceModel

sampleN(int) - Method in class jbil.sequence.AbstractFixedLengthSequenceModel

sampleN(int) - Method in interface jbil.sequence.FixedLengthSequenceModel

Samples a set of i.i.d.

sampleN(int, int) - Method in interface jbil.sequence.SequenceModel

Samples a set of i.i.d.

second - Variable in class jbil.common.Pair

The second element

Sequence - Class in jbil.sequence

Abstract class representing a sequence of symbols from a fixed alphabet.

Sequence() - Constructor for class jbil.sequence.Sequence

sequence(int, int) - Static method in class jbil.util.ArrayUtilities

Returns an int array with succesive elements.

sequenceCount() - Method in interface jbil.sequence.KMerCounter

Returns the number of sequences over which kmers are counted.

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

Returns the total number of sequences represented by this trie, taking into account word multiplicity and high order symbols.

sequenceCount() - Method in class jbil.sequence.TrieForest

Returns the total number of words represented by the active tries in the forest, taking into account word multiplicity and high order symbols.

SequenceFactory - Class in jbil.sequence

Singleton sequence factory.

SequenceModel - Interface in jbil.sequence

Generic interface for a sequence model.

set(int, Symbol) - Method in class jbil.sequence.Alphabet

Replaces the symbol at a given position.

setActiveTrie(int, boolean) - Method in class jbil.sequence.TrieForest

Sets the status of the trie at a given position in the forest active/inactive.

setInput(String, Object) - Method in class jbil.common.AbstractAlgorithm

setInput(String, Object) - Method in interface jbil.common.Algorithm

Sets an input to the algorithm.

setInputs(Map<String, Object>) - Method in class jbil.common.AbstractAlgorithm

setInputs(Map<String, Object>) - Method in interface jbil.common.Algorithm

Sets multiple inputs to the algorithm.

setName(String) - Method in class jbil.sequence.Sequence

Sets the name of the sequence.

setObservedDataWeight(double) - Method in class jbil.sequence.MarkovFixedLengthSequenceModel

A uniform pseudocount of ~ [length-order-1]/[samplesize^observedDataWeight] is added to each kmer.

setPvalueMode(int) - Method in class jbil.sequence.MarkovFixedLengthSequenceModel

Sets the p-value computation mode.

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

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

Sets the symbol at a given position in this sequence.

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

shuffle(int) - Static method in class jbil.util.RandomUtilities

Creates an array containing the elements 0...N-1 in random order.

shuffle(int[]) - Static method in class jbil.util.RandomUtilities

Shuffles an int array.

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

sortIndexes(double[]) - Static method in class jbil.util.ArrayUtilities

Sorts the elements of an array and returns their indexes in order.

startsWith(Sequence) - Method in class jbil.sequence.Sequence

Checks if this sequence begins with a given prefix.

subArray(int[], boolean[]) - Static method in class jbil.util.ArrayUtilities

Return the subarray of an int array by picking the entries indicated by true entries of a boolean mask array of the same size.

subArray(double[], boolean[]) - Static method in class jbil.util.ArrayUtilities

Return the subarray of a double array by picking the entries indicated by true entries of a boolean mask array of the same size.

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

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

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

Gets a new sequence that is a suffix of this sequence.

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

Gets a new sequence that is a subsequence of this sequence.

subSequence(int) - Method in class jbil.sequence.SymbolArraySequence

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

sum(int[]) - Static method in class jbil.util.ArrayUtilities

Returns the sum of the elements of an int array.

Symbol - Interface in jbil.sequence

The unit component of sequences.

SymbolArraySequence - Class in jbil.sequence

Basic high-level implementation of Sequence using an array of symbols.

SymbolArraySequence(Alphabet) - Constructor for class jbil.sequence.SymbolArraySequence

Creates an empty sequence over a given alphabet.

SymbolArraySequence(Alphabet, int) - Constructor for class jbil.sequence.SymbolArraySequence

Creates an empty sequence with a given initial capacity over a given alphabet.

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

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

Gets the symbol at a given position in the sequence.

symbolAt(int) - Method in class jbil.sequence.SymbolArraySequence