Uses of Interface org.biojava.bio.dist.Distribution (BioJava-1.5-beta API)

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

Packages that use Distribution
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.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
`interface` | `OrderNDistribution` Provides an N'th order distribution.

Classes in org.biojava.bio.dist that implement Distribution
`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
`static Distribution` | `DistributionTools.average(Distribution[] dists)` Averages two or more distributions.
`static Distribution` | `DistributionTools.countToDistribution(Count c)` Make a distribution from a count.
`Distribution` | `OrderNDistributionFactory.createDistribution(Alphabet alpha)` Creates an OrderNDistribution of the appropriate type.
`Distribution` | `DistributionFactory.createDistribution(Alphabet alpha)` Generate a new Distribution as requested.
`Distribution` | `DistributionFactory.DefaultDistributionFactory.createDistribution(Alphabet alpha)`
`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` | `GapDistribution.getNullModel()`
`Distribution` | `Distribution.getNullModel()` Retrieve the null model Distribution that this Distribution recognizes.
`Distribution` | `TranslatedDistribution.getNullModel()`
`Distribution` | `AbstractOrderNDistribution.getNullModel()`
`Distribution` | `PairDistribution.getNullModel()`
`Distribution` | `UniformDistribution.getNullModel()`
`Distribution` | `SimpleDistribution.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
`void` | `DistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times)` Registers that sym was counted in this state.
`void` | `SimpleDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times)`
`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` | `DistributionTrainerContext.getCount(Distribution dist, Symbol sym)` Return the number of counts of a particular symbol which will be used to train the specified distribution.
`double` | `SimpleDistributionTrainerContext.getCount(Distribution dist, Symbol sym)`
`protected static Distribution` | `PairDistribution.getNullModel(Distribution first, Distribution second)` Get a uniform null model over a PairDistribution over [first,second].
`DistributionTrainer` | `DistributionTrainerContext.getTrainer(Distribution dist)` Return the Distribution trainer object from the current context.
`DistributionTrainer` | `SimpleDistributionTrainerContext.getTrainer(Distribution dist)`
`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` | `DistributionTrainerContext.registerDistribution(Distribution dist)` Register a distribution object with this context.
`void` | `SimpleDistributionTrainerContext.registerDistribution(Distribution dist)`
`void` | `DistributionTrainerContext.registerTrainer(Distribution dist, DistributionTrainer trainer)` Register a Distribution and an associated DistributionTrainer object.
`void` | `SimpleDistributionTrainerContext.registerTrainer(Distribution dist, DistributionTrainer trainer)`
`void` | `OrderNDistribution.setDistribution(Symbol sym, Distribution dist)` Set the distribution assocated with a symbol.
`void` | `AbstractDistribution.setNullModel(Distribution nullModel)`
`void` | `GapDistribution.setNullModel(Distribution nullModel)`
`void` | `Distribution.setNullModel(Distribution nullDist)` Set the null model Distribution that this Distribution recognizes.
`void` | `TranslatedDistribution.setNullModel(Distribution dist)`
`void` | `PairDistribution.setNullModel(Distribution nullModel)`
`protected abstract void` | `AbstractDistribution.setNullModelImpl(Distribution nullModel)` Implement this to set the null model.
`void` | `AbstractOrderNDistribution.setNullModelImpl(Distribution nullModel)`
`protected void` | `UniformDistribution.setNullModelImpl(Distribution nullModel)` Assign a background distribution.
`protected void` | `SimpleDistribution.setNullModelImpl(Distribution nullModel)`
`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
`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
`Distribution` | `SimpleWeightMatrix.getColumn(int column)`
`Distribution` | `WeightMatrix.getColumn(int column)` Retrieve a column as an EmissionState.
`Distribution` | `SimpleEmissionState.getDistribution()`
`Distribution` | `EmissionState.getDistribution()` Get the Distribution associated with this state.
`Distribution` | `WMAsMM.getWeights(State source)`
`Distribution` | `SimpleMarkovModel.getWeights(State source)`
`Distribution` | `MarkovModel.getWeights(State source)` Get a probability Distribution over the transition from 'source'.

Methods in org.biojava.bio.dp with parameters of type Distribution
`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` | `SimpleEmissionState.setDistribution(Distribution dis)`
`void` | `EmissionState.setDistribution(Distribution dis)` Set the Distribution associated with this state.
`void` | `WMAsMM.setWeights(State source, Distribution dist)`
`void` | `SimpleMarkovModel.setWeights(State source, Distribution dist)` Use this methods to customize the transition probabilities.
`void` | `MarkovModel.setWeights(State source, Distribution dist)` Set the probability distribution over the transitions from 'source'.

Constructors in org.biojava.bio.dp with parameters of type Distribution
`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
`Distribution` | `DistributionLogo.getDistribution()` Retrieve the currently rendered dist.
`Distribution` | `LogoContext.getDistribution()`

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

Methods in org.biojava.bio.program.hmmer with parameters of type Distribution
`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
`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
`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
`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
`Distribution` | `CodonPref.getFrequency()` returns a Distribution giving the frequency of codons (sums to one over the totality of codons).
`Distribution` | `SimpleCodonPref.getFrequency()`
`Distribution` | `CodonPref.getFrequencyForSynonyms(Symbol residue)` returns a Distribution giving the frequency of synonymous codons.
`Distribution` | `SimpleCodonPref.getFrequencyForSynonyms(Symbol residue)`
`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
`SimpleCodonPref(String geneticCodeName, Distribution codonPref, String name)`

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