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

C

c - Static variable in class jbil.sequence.DNAAlphabet

The atomic 'c' symbol

c() - Method in class jbil.sequence.DNAAlphabet

c - Static variable in class jbil.sequence.ExtendedDNAAlphabet

The atomic 'a' symbol

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

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

CharSymbol - Class in jbil.sequence

Abstract class for symbols associated to a character (either atomic or higher order).

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

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

charValue() - Method in class jbil.sequence.CharSymbol

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

clone() - Method in class jbil.sequence.ByteArraySequence

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

clone() - Method in class jbil.sequence.SymbolArraySequence

contains(Object) - Method in class jbil.common.Pair

Checks if the pair contains one given element.

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

CONVERGED - Static variable in class jbil.sequence.GibbsMotifSiteSampler

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

countOccurrences(Sequence, int, int, int) - Method in interface jbil.sequence.KMerCounter

Counts the number of occurrences of the kmers pattern[beginIndex..endIndex-2] and pattern[beginIndex..endIndex-1] respectively, from a given position in a set of sequences.

countOccurrences(Sequence, int, int, Trie.TrieNode) - Method in class jbil.sequence.Trie

Counts the number of occurrences of the patterns pattern[beginIndex..endIndex-2] and pattern[beginIndex..endIndex-1] respectively, as prefixes of the words represented by the subtrie rooted at a given node.

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

Counts the number of occurrences of the patterns pattern[beginIndex..endIndex-2] and pattern[beginIndex..endIndex-1] respectively, as prefixes of the words represented by the subtries rooted at nodes at a given height.

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

Counts the number of occurrences of the patterns pattern[beginIndex..endIndex-2] and pattern[beginIndex..endIndex-1] respectively, as prefixes of words represented by the subtries of the active tries in the forest rooted at nodes at a given height.

createDNASequence(String) - Method in class jbil.sequence.SequenceFactory

Parses a string into a DNA sequence, that is, a Sequence object.