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

P

Pair<E,F> - Class in jbil.common

Utility 'generalised' class representing a pair of values with not necessarily identical types.

Pair() - Constructor for class jbil.common.Pair

Creates a new (null,null) pair.

Pair(E, F) - Constructor for class jbil.common.Pair

Creates a new pair with specified elements.

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

Pick integers at random with equal probabilities and without repositions in the range from 0 up to a given upper limit (not inclusive).

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

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

Computes the probability of observing a letter in a given position of the sequence.

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

prefixLikelihood(Sequence) - Method in class jbil.sequence.AbstractFixedLengthSequenceModel

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

prefixLikelihood(Sequence) - Method in interface jbil.sequence.SequenceModel

returns the likelihod of the given prefix under this model, that is, the sum of the probabilities of all words starting with the given prefix.

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

Returns the likelihod of the given prefix under this model, that is, the sum of the probabilities of all words starting with the subword of sequence starting at position beginIndex and ending at position endIndex-1.

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

prepend(Symbol) - Method in class jbil.sequence.ByteArraySequence

prepend(Sequence) - Method in class jbil.sequence.ByteArraySequence

prepend(Symbol) - Method in class jbil.sequence.Sequence

Prepends a symbol to this sequence.

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

Prepends a sequence to this sequence.

prepend(Symbol) - Method in class jbil.sequence.SymbolArraySequence

prepend(Sequence) - Method in class jbil.sequence.SymbolArraySequence

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

Prints a string representation of the trie to System.out.

printArray(double[]) - Static method in class jbil.util.ArrayPrinter

Prints a double array in standard output.

printArray(PrintStream, String, String, String, String, double[]) - Static method in class jbil.util.ArrayPrinter

Prints a double array.

printArray(PrintWriter, String, String, String, String, double[]) - Static method in class jbil.util.ArrayPrinter

Prints a double array.

printArray(int[]) - Static method in class jbil.util.ArrayPrinter

Prints an int array with a given name in standard output.

printArray(PrintStream, String, String, String, String, int[]) - Static method in class jbil.util.ArrayPrinter

Prints an int array.

printArray(PrintWriter, String, String, String, String, int[]) - Static method in class jbil.util.ArrayPrinter

Prints an int array.

printAsRArray(PrintStream, String, String, double[]) - Static method in class jbil.util.ArrayPrinter

Prints a double array as a R array definition.

printAsRArray(PrintStream, String, String, Double[]) - Static method in class jbil.util.ArrayPrinter

Prints a Double array as a R array definition.

printAsRMatrix(PrintStream, String, String, double[][]) - Static method in class jbil.util.ArrayPrinter

Prints a double bi-dimensional array as a R matrix definition.

printAsRMatrix(PrintStream, String, String, Double[][]) - Static method in class jbil.util.ArrayPrinter

Prints a Double bi-dimensional array as a R matrix definition.

prob(int) - Method in class jbil.rv.IntIntervalDist

pvalue(Sequence) - Method in class jbil.sequence.AbstractFixedLengthSequenceModel

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

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

pvalue(Sequence, SequenceModel) - Method in class jbil.sequence.AbstractFixedLengthSequenceModel

pvalue(Sequence, int, int, SequenceModel) - Method in class jbil.sequence.AbstractFixedLengthSequenceModel

pvalue(Sequence, int) - Method in interface jbil.sequence.FixedLengthSequenceModel

Returns the p-value of the subword of the given word starting at beginIndex and of the appropriate length with a default null model (typically the uniform model).

pvalue(Sequence, int, SequenceModel) - Method in interface jbil.sequence.FixedLengthSequenceModel

Returns the p-value of the subword of the given word starting at beginIndex and with the appropriate length.

pvalue(Sequence, int, SequenceModel) - Method in class jbil.sequence.MarkovFixedLengthSequenceModel

pvalue(Sequence) - Method in interface jbil.sequence.SequenceModel

Returns the p-value of the given word with a default null model (usually the uniform null model).

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

Returns the p-value of the subword of the given word starting at beginIndex and ending at endIndex-1 with a default null model (typically the uniform model).

pvalue(Sequence, SequenceModel) - Method in interface jbil.sequence.SequenceModel

The p-value of a given sequence is defined as the probability under a null model for a sequence to have a likelihood greater or equal to the likelihood of the given sequence under this model.

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

Returns the p-value of the subword of the given word starting at beginIndex and ending at endIndex-1.

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

pvalue(Sequence, int, SequenceModel) - Method in class jbil.sequence.UniformFixedLengthSequenceModel

PVALUE_BRANCH_AND_BOUND - Static variable in class jbil.sequence.MarkovFixedLengthSequenceModel

Branch & bound p-value computation mode.

PVALUE_BRUTE_FORCE - Static variable in class jbil.sequence.MarkovFixedLengthSequenceModel

Brute force p-value computation mode.

PVALUE_ITERATIVE_REFINEMENT - Static variable in class jbil.sequence.MarkovFixedLengthSequenceModel

Iterative refinememnt p-value computation mode.