Uses of Class
jbil.sequence.Sequence

Packages that use Sequence

jbil.sequence

Uses of Sequence in jbil.sequence

Subclasses of Sequence in jbil.sequence

class	ByteArraySequence Implementation of Sequence in which the sequence of symbols is translated into an array of bytes s.t.
class	SymbolArraySequence Basic high-level implementation of Sequence using an array of symbols.

Methods in jbil.sequence that return Sequence

Sequence	SymbolArraySequence.clone()
abstract Sequence	Sequence.clone()
Sequence	ByteArraySequence.clone()
Sequence	SequenceFactory.createDNASequence(java.lang.String strsequence) Parses a string into a DNA sequence, that is, a Sequence object.
Sequence	SequenceFactory.newSequence(Alphabet alphabet) Creates a new empty sequence over the specified base alphabet.
Sequence	UniformFixedLengthSequenceModel.sample()
Sequence	MarkovFixedLengthSequenceModel.sample()
Sequence	FixedLengthSequenceModel.sample() Samples a sequence with the apropriate length from this model.
Sequence	SequenceModel.sample(int length) Samples a sequence from this model.
Sequence	AbstractFixedLengthSequenceModel.sample(int length)
Sequence[]	FixedLengthSequenceModel.sampleN(int sampleSize) Samples a set of i.i.d.
Sequence[]	AbstractFixedLengthSequenceModel.sampleN(int sampleSize)
Sequence[]	SequenceModel.sampleN(int sampleSize, int length) Samples a set of i.i.d.
Sequence[]	AbstractFixedLengthSequenceModel.sampleN(int sampleSize, int length)
Sequence	SymbolArraySequence.subSequence(int beginIndex)
abstract Sequence	Sequence.subSequence(int beginIndex) Gets a new sequence that is a suffix of this sequence.
Sequence	ByteArraySequence.subSequence(int beginIndex)
Sequence	SymbolArraySequence.subSequence(int beginIndex, int endIndex)
abstract Sequence	Sequence.subSequence(int beginIndex, int endIndex) Gets a new sequence that is a subsequence of this sequence.
Sequence	ByteArraySequence.subSequence(int beginIndex, int endIndex)

Methods in jbil.sequence that return types with arguments of type Sequence

java.util.List<Sequence>

Trie.getSequenceList() Returns the list of sequences represented by this trie.

Methods in jbil.sequence with parameters of type Sequence

void	FactorTrie.addBaseSequence(Sequence baseSequence) Adds a base sequence to the factor trie, i.e., add all factors of the adequate size of this sequence to the trie.
jbil.sequence.Trie.TrieNode	Trie.addSequence(Sequence sequence) Adds a sequence to the trie and returns its locus.
jbil.sequence.Trie.TrieNode	Trie.addSequence(Sequence sequence, int beginIndex, int endIndex) Adds a sequence to the trie and returns its locus.
void	SymbolArraySequence.append(Sequence sequence)
abstract void	Sequence.append(Sequence sequence) Appends a sequence to this sequence.
void	ByteArraySequence.append(Sequence sequence)
Pair<java.lang.Integer,java.lang.Integer>	TrieForest.countOccurrences(Sequence pattern, int beginIndex, int endIndex, int offset) 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.
Pair<java.lang.Integer,java.lang.Integer>	Trie.countOccurrences(Sequence pattern, int beginIndex, int endIndex, int offset) 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.
Pair<java.lang.Integer,java.lang.Integer>	KMerCounter.countOccurrences(Sequence pattern, int beginIndex, int endIndex, int offset) 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.
Pair<java.lang.Integer,java.lang.Integer>	FactorTrie.countOccurrences(Sequence pattern, int beginIndex, int endIndex, int offset)
Pair<java.lang.Integer,java.lang.Integer>	Trie.countOccurrences(Sequence pattern, int beginIndex, int endIndex, jbil.sequence.Trie.TrieNode node) 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.
boolean	Trie.deleteSequence(Sequence sequence) Removes a sequence from the trie provided that it belongs to the (multi)set of sequences represented by the trie.
boolean	Trie.deleteSequence(Sequence sequence, int beginIndex, int endIndex) Deletes a subsequence of a given sequence from the trie.
boolean	Sequence.endsWith(Sequence subSequence) Checks if this sequence ends with a given suffix.
void	SymbolArraySequence.insert(int index, Sequence sequence)
abstract void	Sequence.insert(int index, Sequence sequence) Inserts a sequence at a given position in this sequence.
void	ByteArraySequence.insert(int index, Sequence sequence)
double	SequenceModel.likelihood(Sequence word) Returns the likelihod of the given word under this model.
double	AbstractFixedLengthSequenceModel.likelihood(Sequence word)
double	UniformFixedLengthSequenceModel.likelihood(Sequence word, int beginIndex)
double	MarkovFixedLengthSequenceModel.likelihood(Sequence word, int beginIndex)
double	FixedLengthSequenceModel.likelihood(Sequence word, int beginIndex) Returns the likelihod of the subword of the given word starting at beginIndex and with the appropriate length.
double	SequenceModel.likelihood(Sequence word, int beginIndex, int endIndex) Returns the likelihod of the subword of the given word starting at beginIndex and ending at endIndex-1.
double	AbstractFixedLengthSequenceModel.likelihood(Sequence word, int beginIndex, int endIndex)
boolean	Sequence.occursAt(Sequence subSequence, int beginIndex) Checks if a sequence occurs at a specified position of this sequence.
double	UniformFixedLengthSequenceModel.positionProbability(int position, Sequence neighbourhoodSeq, int beginIndex, int endIndex, int letterPosition)
double	SequenceModel.positionProbability(int position, Sequence neighbourhoodSeq, int beginIndex, int endIndex, int letterPosition) Computes the probability of observing a letter in a given position of the sequence.
double	MarkovFixedLengthSequenceModel.positionProbability(int position, Sequence neighbourhoodSeq, int beginIndex, int endIndex, int letterPosition)
double	SequenceModel.prefixLikelihood(Sequence sequence) 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.
double	AbstractFixedLengthSequenceModel.prefixLikelihood(Sequence sequence)
double	UniformFixedLengthSequenceModel.prefixLikelihood(Sequence sequence, int beginIndex, int endIndex)
double	SequenceModel.prefixLikelihood(Sequence sequence, int beginIndex, int endIndex) 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.
double	MarkovFixedLengthSequenceModel.prefixLikelihood(Sequence sequence, int beginIndex, int endIndex)
void	SymbolArraySequence.prepend(Sequence sequence)
abstract void	Sequence.prepend(Sequence sequence) Prepends a sequence to this sequence.
void	ByteArraySequence.prepend(Sequence sequence)
double	SequenceModel.pvalue(Sequence word) Returns the p-value of the given word with a default null model (usually the uniform null model).
double	AbstractFixedLengthSequenceModel.pvalue(Sequence word)
double	UniformFixedLengthSequenceModel.pvalue(Sequence word, int beginIndex)
double	FixedLengthSequenceModel.pvalue(Sequence word, int beginIndex) 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).
double	AbstractFixedLengthSequenceModel.pvalue(Sequence word, int beginIndex)
double	SequenceModel.pvalue(Sequence word, int beginIndex, int endIndex) 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).
double	AbstractFixedLengthSequenceModel.pvalue(Sequence word, int beginIndex, int endIndex)
double	SequenceModel.pvalue(Sequence word, int beginIndex, int endIndex, SequenceModel nullModel) Returns the p-value of the subword of the given word starting at beginIndex and ending at endIndex-1.
double	AbstractFixedLengthSequenceModel.pvalue(Sequence word, int beginIndex, int endIndex, SequenceModel nullModel)
double	UniformFixedLengthSequenceModel.pvalue(Sequence word, int beginIndex, SequenceModel nullModel)
double	MarkovFixedLengthSequenceModel.pvalue(Sequence word, int beginIndex, SequenceModel nullModel)
double	FixedLengthSequenceModel.pvalue(Sequence word, int beginIndex, SequenceModel nullModel) Returns the p-value of the subword of the given word starting at beginIndex and with the appropriate length.
double	SequenceModel.pvalue(Sequence word, SequenceModel nullModel) 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.
double	AbstractFixedLengthSequenceModel.pvalue(Sequence word, SequenceModel nullModel)
void	FactorTrie.removeBaseSequence(Sequence baseSequence) 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.
boolean	Sequence.startsWith(Sequence subSequence) Checks if this sequence begins with a given prefix.

Constructors in jbil.sequence with parameters of type Sequence

FactorTrie(Sequence baseSequence, int factorLength)
Creates a factor trie representing the factors of a given sequence.