Uses of Interface
org.biojava.bio.dist.Distribution

Packages that use Distribution

Package	Description
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.gui	Graphical interfaces for biojava objects.
org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program.fastq	FASTQ and variants sequence format I/O.
org.biojava.bio.program.hmmer	Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.

Uses of Distribution in org.biojava.bio.dist

Subinterfaces of Distribution in org.biojava.bio.dist

Modifier and Type	Interface and Description
interface	OrderNDistribution Provides an N'th order distribution.

Classes in org.biojava.bio.dist that implement Distribution

Modifier and Type	Class and Description
class	AbstractDistribution An abstract implementation of Distribution.
class	AbstractOrderNDistribution Simple base class for OrderNDistributions.
class	GapDistribution This distribution emits gap symbols.
class	PairDistribution Class for pairing up two independant distributions.
class	SimpleDistribution A simple implementation of a distribution, which works with any finite alphabet.
class	TranslatedDistribution A translated view of some underlying distribution.
class	UniformDistribution An implementation of an uniform distribution
class	UntrainableDistribution A distribution which does not interact with the training framework.

Methods in org.biojava.bio.dist that return Distribution

Modifier and Type	Method and Description
static Distribution	DistributionTools.average(Distribution[] dists) Averages two or more distributions.
static Distribution	DistributionTools.countToDistribution(Count c) Make a distribution from a count.
Distribution	DistributionFactory.createDistribution(Alphabet alpha) Generate a new Distribution as requested.
Distribution	DistributionFactory.DefaultDistributionFactory.createDistribution(Alphabet alpha)
Distribution	OrderNDistributionFactory.createDistribution(Alphabet alpha) Creates an OrderNDistribution of the appropriate type.
static Distribution[]	DistributionTools.distOverAlignment(Alignment a) Equivalent to distOverAlignment(a, false, 0.0).
static Distribution[]	DistributionTools.distOverAlignment(Alignment a, boolean countGaps) Creates an array of distributions, one for each column of the alignment.
static Distribution[]	DistributionTools.distOverAlignment(Alignment a, boolean countGaps, double nullWeight) Creates an array of distributions, one for each column of the alignment.
Distribution	OrderNDistribution.getDistribution(Symbol sym)
Distribution	UniformDistribution.getNullModel()
Distribution	TranslatedDistribution.getNullModel()
Distribution	SimpleDistribution.getNullModel()
Distribution	Distribution.getNullModel() Retrieve the null model Distribution that this Distribution recognizes.
Distribution	GapDistribution.getNullModel()
Distribution	AbstractOrderNDistribution.getNullModel()
Distribution	PairDistribution.getNullModel()
protected static Distribution	PairDistribution.getNullModel(Distribution first, Distribution second) Get a uniform null model over a PairDistribution over [first,second].
static Distribution	DistributionTools.jointDistOverAlignment(Alignment a, boolean countGaps, double nullWeight, int[] cols) Creates a joint distribution.
Distribution	XMLDistributionReader.parseXML(InputStream is) Reads an XML representation of a Distribution from a file.
static Distribution	DistributionTools.readFromXML(InputStream is) Read a distribution from XML.

Methods in org.biojava.bio.dist with parameters of type Distribution

Modifier and Type	Method and Description
void	SimpleDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times)
void	DistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times) Registers that sym was counted in this state.
static boolean	DistributionTools.areEmissionSpectraEqual(Distribution[] a, Distribution[] b) Compares the emission spectra of two distribution arrays.
static boolean	DistributionTools.areEmissionSpectraEqual(Distribution[] a, Distribution[] b) Compares the emission spectra of two distribution arrays.
static boolean	DistributionTools.areEmissionSpectraEqual(Distribution a, Distribution b) Compares the emission spectra of two distributions.
static Distribution	DistributionTools.average(Distribution[] dists) Averages two or more distributions.
static double	DistributionTools.bitsOfInformation(Distribution observed) Calculates the total bits of information for a distribution.
static Sequence	DistributionTools.generateSequence(String name, Distribution d, int length) Produces a sequence by randomly sampling the Distribution.
static SymbolList	DistributionTools.generateSymbolList(Distribution d, int length) Produces a SymbolList by randomly sampling a Distribution.
double	SimpleDistributionTrainerContext.getCount(Distribution dist, Symbol sym)
double	DistributionTrainerContext.getCount(Distribution dist, Symbol sym) Return the number of counts of a particular symbol which will be used to train the specified distribution.
protected static Distribution	PairDistribution.getNullModel(Distribution first, Distribution second) Get a uniform null model over a PairDistribution over [first,second].
DistributionTrainer	SimpleDistributionTrainerContext.getTrainer(Distribution dist)
DistributionTrainer	DistributionTrainerContext.getTrainer(Distribution dist) Return the Distribution trainer object from the current context.
static HashMap	DistributionTools.KLDistance(Distribution observed, Distribution expected, double logBase) A method to calculate the Kullback-Liebler Distance (relative entropy).
static void	DistributionTools.randomizeDistribution(Distribution d) Randomizes the weights of a Distribution.
void	SimpleDistributionTrainerContext.registerDistribution(Distribution dist)
void	DistributionTrainerContext.registerDistribution(Distribution dist) Register a distribution object with this context.
void	SimpleDistributionTrainerContext.registerTrainer(Distribution dist, DistributionTrainer trainer)
void	DistributionTrainerContext.registerTrainer(Distribution dist, DistributionTrainer trainer) Register a Distribution and an associated DistributionTrainer object.
void	OrderNDistribution.setDistribution(Symbol sym, Distribution dist) Set the distribution assocated with a symbol.
void	TranslatedDistribution.setNullModel(Distribution dist)
void	Distribution.setNullModel(Distribution nullDist) Set the null model Distribution that this Distribution recognizes.
void	GapDistribution.setNullModel(Distribution nullModel)
void	PairDistribution.setNullModel(Distribution nullModel)
void	AbstractDistribution.setNullModel(Distribution nullModel)
protected void	UniformDistribution.setNullModelImpl(Distribution nullModel) Assign a background distribution.
protected void	SimpleDistribution.setNullModelImpl(Distribution nullModel)
void	AbstractOrderNDistribution.setNullModelImpl(Distribution nullModel)
protected abstract void	AbstractDistribution.setNullModelImpl(Distribution nullModel) Implement this to set the null model.
static HashMap	DistributionTools.shannonEntropy(Distribution observed, double logBase) A method to calculate the Shannon Entropy for a Distribution.
static double	DistributionTools.totalEntropy(Distribution observed) Calculates the total Entropy for a Distribution.
void	XMLDistributionWriter.writeDistribution(Distribution d, OutputStream os) Writes an OrderNDistribution or simple Distribution to an XML file.
static void	DistributionTools.writeToXML(Distribution d, OutputStream os) Writes a Distribution to XML that can be read with the readFromXML method.

Constructors in org.biojava.bio.dist with parameters of type Distribution

Constructor and Description
PairDistribution(Distribution first, Distribution second) Create a new PairDistribution that represents the product of two other distributions.
SimpleDistribution(Distribution dist) make an instance of SimpleDistribution with weights identical to the specified Distribution.
SimpleDistributionTrainer(Distribution dis) Deprecated.
TranslatedDistribution(ReversibleTranslationTable table, Distribution other, DistributionFactory distFact) Create a new TranslatedDistribution.

Uses of Distribution in org.biojava.bio.dp

Methods in org.biojava.bio.dp that return Distribution

Modifier and Type	Method and Description
Distribution	SimpleWeightMatrix.getColumn(int column)
Distribution	WeightMatrix.getColumn(int column) Retrieve a column as an EmissionState.
Distribution	EmissionState.getDistribution() Get the Distribution associated with this state.
Distribution	SimpleEmissionState.getDistribution()
Distribution	WMAsMM.getWeights(State source)
Distribution	MarkovModel.getWeights(State source) Get a probability Distribution over the transition from 'source'.
Distribution	SimpleMarkovModel.getWeights(State source)

Methods in org.biojava.bio.dp with parameters of type Distribution

Modifier and Type	Method and Description
double	ScoreType.calculateScore(Distribution dist, Symbol sym) Calculates the score associated with a distribution and a symbol.
double	ScoreType.Probability.calculateScore(Distribution dist, Symbol sym)
double	ScoreType.Odds.calculateScore(Distribution dist, Symbol sym)
double	ScoreType.NullModel.calculateScore(Distribution dist, Symbol sym)
void	EmissionState.setDistribution(Distribution dis) Set the Distribution associated with this state.
void	SimpleEmissionState.setDistribution(Distribution dis)
void	WMAsMM.setWeights(State source, Distribution dist)
void	MarkovModel.setWeights(State source, Distribution dist) Set the probability distribution over the transitions from 'source'.
void	SimpleMarkovModel.setWeights(State source, Distribution dist) Use this methods to customize the transition probabilities.

Constructors in org.biojava.bio.dp with parameters of type Distribution

Constructor and Description
SimpleEmissionState(String name, Annotation ann, int[] advance, Distribution dis)
SimpleWeightMatrix(Distribution[] columns)

Uses of Distribution in org.biojava.bio.gui

Methods in org.biojava.bio.gui that return Distribution

Modifier and Type	Method and Description
Distribution	LogoContext.getDistribution()
Distribution	DistributionLogo.getDistribution() Retrieve the currently rendered dist.

Methods in org.biojava.bio.gui with parameters of type Distribution

Modifier and Type	Method and Description
static double	DistributionLogo.entropy(Distribution dist, Symbol s) Calculate the information content of a symbol in bits.
void	DistributionLogo.setDistribution(Distribution dist) Set the dist to render.
static double	DistributionLogo.totalBits(Distribution dist) Retrieve the maximal number of bits possible for this type of dist.
static double	DistributionLogo.totalInformation(Distribution dist) Calculates the total information of the dist in bits.

Uses of Distribution in org.biojava.bio.molbio

Methods in org.biojava.bio.molbio that return Distribution

Modifier and Type	Method and Description
Distribution	Composition.getDistribution() Returns the distribution backing this class.

Uses of Distribution in org.biojava.bio.program.fastq

Methods in org.biojava.bio.program.fastq that return Distribution

Modifier and Type	Method and Description
static Distribution[]	FastqTools.createSymbolDistribution(Fastq fastq) Create and return a new array of symbol Distributions from the specified FASTQ formatted sequence.

Uses of Distribution in org.biojava.bio.program.hmmer

Methods in org.biojava.bio.program.hmmer with parameters of type Distribution

Modifier and Type	Method and Description
protected EmissionState	HmmerProfileHMM.makeNewInsertState(String str, Annotation ann, int[] adv, Distribution dis)
protected EmissionState	HmmerProfileHMM.makeNewMatchState(String str, Annotation ann, int[] adv, Distribution dis)

Constructors in org.biojava.bio.program.hmmer with parameters of type Distribution

Constructor and Description
ProfileEmissionState(String str, Annotation ann, int[] adv, Distribution dis)

Uses of Distribution in org.biojava.bio.program.phred

Methods in org.biojava.bio.program.phred that return Distribution

Modifier and Type	Method and Description
static Distribution[]	PhredTools.phredAlignmentToDistArray(Alignment a) converts an Alignment of PhredSequences to a Distribution[] where each position is the average distribution of the underlying column of the alignment.
static Distribution[]	PhredTools.phredToDistArray(PhredSequence s) Converts a Phred sequence to an array of distributions.

Uses of Distribution in org.biojava.bio.seq

Methods in org.biojava.bio.seq that return Distribution

Modifier and Type	Method and Description
static Distribution	DNATools.getDNADistribution(double fractionGC) return a SimpleDistribution of specified GC content.
static Distribution	DNATools.getDNAxDNADistribution(double fractionGC0, double fractionGC1) return a (DNA x DNA) cross-product Distribution with specified DNA contents in each component Alphabet.

Uses of Distribution in org.biojava.bio.symbol

Methods in org.biojava.bio.symbol that return Distribution

Modifier and Type	Method and Description
Distribution	SimpleCodonPref.getFrequency()
Distribution	CodonPref.getFrequency() returns a Distribution giving the frequency of codons (sums to one over the totality of codons).
Distribution	SimpleCodonPref.getFrequencyForSynonyms(Symbol residue)
Distribution	CodonPref.getFrequencyForSynonyms(Symbol residue) returns a Distribution giving the frequency of synonymous codons.
Distribution	WobbleDistribution.getFrequencyOfNonWobbleBases() returns the frequency with which synonymous codons start with a specified pair of bases.
Distribution	WobbleDistribution.getWobbleFrequency(Symbol nonWobbleBases) returns the frequency of a specific wobble base in a set of synonymous codons that start with the same two bases.

Constructors in org.biojava.bio.symbol with parameters of type Distribution

Constructor and Description
SimpleCodonPref(String geneticCodeName, Distribution codonPref, String name)