Uses of Interface
org.biojava.bio.dist.Distribution
Packages that use Distribution
Package
Description
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
FASTQ and variants sequence format I/O.
Tools for working with profile Hidden Markov Models from the HMMer package.
Parser for Phred output
Classes and interfaces for defining biological sequences and informatics
objects.
Representation of the Symbols that make up a sequence, and locations within
them.
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Uses of Distribution in org.biojava.bio.dist
Subinterfaces of Distribution in org.biojava.bio.distModifier and TypeInterfaceDescriptioninterface
Provides an N'th order distribution.Classes in org.biojava.bio.dist that implement DistributionModifier and TypeClassDescriptionclass
An abstract implementation of Distribution.class
Simple base class for OrderNDistributions.class
This distribution emits gap symbols.class
Class for pairing up two independant distributions.class
A simple implementation of a distribution, which works with any finite alphabet.class
A translated view of some underlying distribution.class
An implementation of an uniform distributionclass
A distribution which does not interact with the training framework.Methods in org.biojava.bio.dist that return DistributionModifier and TypeMethodDescriptionstatic final Distribution
DistributionTools.average
(Distribution[] dists) Averages two or more distributions.static Distribution
DistributionTools.countToDistribution
(Count c) Make a distribution from a count.DistributionFactory.createDistribution
(Alphabet alpha) Generate a new Distribution as requested.DistributionFactory.DefaultDistributionFactory.createDistribution
(Alphabet alpha) 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 final Distribution[]
DistributionTools.distOverAlignment
(Alignment a, boolean countGaps) Creates an array of distributions, one for each column of the alignment.static final Distribution[]
DistributionTools.distOverAlignment
(Alignment a, boolean countGaps, double nullWeight) Creates an array of distributions, one for each column of the alignment.OrderNDistribution.getDistribution
(Symbol sym) AbstractOrderNDistribution.getNullModel()
Distribution.getNullModel()
Retrieve the null model Distribution that this Distribution recognizes.GapDistribution.getNullModel()
PairDistribution.getNullModel()
protected static Distribution
PairDistribution.getNullModel
(Distribution first, Distribution second) Get a uniform null model over a PairDistribution over [first,second].SimpleDistribution.getNullModel()
TranslatedDistribution.getNullModel()
UniformDistribution.getNullModel()
static final Distribution
DistributionTools.jointDistOverAlignment
(Alignment a, boolean countGaps, double nullWeight, int[] cols) Creates a joint 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 DistributionModifier and TypeMethodDescriptionvoid
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 final boolean
DistributionTools.areEmissionSpectraEqual
(Distribution[] a, Distribution[] b) Compares the emission spectra of two distribution arrays.static final boolean
DistributionTools.areEmissionSpectraEqual
(Distribution a, Distribution b) Compares the emission spectra of two distributions.static final Distribution
DistributionTools.average
(Distribution[] dists) Averages two or more distributions.static final double
DistributionTools.bitsOfInformation
(Distribution observed) Calculates the total bits of information for a distribution.static final Sequence
DistributionTools.generateSequence
(String name, Distribution d, int length) Produces a sequence by randomly sampling the Distribution.static final SymbolList
DistributionTools.generateSymbolList
(Distribution d, int length) Produces aSymbolList
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].DistributionTrainerContext.getTrainer
(Distribution dist) Return the Distribution trainer object from the current context.SimpleDistributionTrainerContext.getTrainer
(Distribution dist) static final 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 aDistribution
.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.final void
AbstractDistribution.setNullModel
(Distribution nullModel) 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
TranslatedDistribution.setNullModel
(Distribution dist) protected abstract void
AbstractDistribution.setNullModelImpl
(Distribution nullModel) Implement this to set the null model.void
AbstractOrderNDistribution.setNullModelImpl
(Distribution nullModel) protected void
SimpleDistribution.setNullModelImpl
(Distribution nullModel) protected void
UniformDistribution.setNullModelImpl
(Distribution nullModel) Assign a background distribution.static final 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 DistributionModifierConstructorDescriptionPairDistribution
(Distribution first, Distribution second) Create a new PairDistribution that represents the product of two other distributions.make an instance of SimpleDistribution with weights identical to the specified Distribution.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 DistributionModifier and TypeMethodDescriptionSimpleWeightMatrix.getColumn
(int column) WeightMatrix.getColumn
(int column) Retrieve a column as an EmissionState.EmissionState.getDistribution()
Get the Distribution associated with this state.final Distribution
SimpleEmissionState.getDistribution()
MarkovModel.getWeights
(State source) Get a probability Distribution over the transition from 'source'.SimpleMarkovModel.getWeights
(State source) WMAsMM.getWeights
(State source) Methods in org.biojava.bio.dp with parameters of type DistributionModifier and TypeMethodDescriptiondouble
ScoreType.calculateScore
(Distribution dist, Symbol sym) Calculates the score associated with a distribution and a symbol.double
ScoreType.NullModel.calculateScore
(Distribution dist, Symbol sym) double
ScoreType.Odds.calculateScore
(Distribution dist, Symbol sym) double
ScoreType.Probability.calculateScore
(Distribution dist, Symbol sym) void
EmissionState.setDistribution
(Distribution dis) Set the Distribution associated with this state.final void
SimpleEmissionState.setDistribution
(Distribution dis) 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.void
WMAsMM.setWeights
(State source, Distribution dist) Constructors in org.biojava.bio.dp with parameters of type DistributionModifierConstructorDescriptionSimpleEmissionState
(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 DistributionModifier and TypeMethodDescriptionDistributionLogo.getDistribution()
Retrieve the currently rendered dist.LogoContext.getDistribution()
Methods in org.biojava.bio.gui with parameters of type DistributionModifier and TypeMethodDescriptionstatic 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 DistributionModifier and TypeMethodDescriptionComposition.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 DistributionModifier and TypeMethodDescriptionstatic Distribution[]
FastqTools.createSymbolDistribution
(Fastq fastq) Create and return a new array of symbolDistribution
s 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 DistributionModifier and TypeMethodDescriptionprotected 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 DistributionModifierConstructorDescriptionProfileEmissionState
(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 DistributionModifier and TypeMethodDescriptionstatic 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 DistributionModifier and TypeMethodDescriptionstatic 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 DistributionModifier and TypeMethodDescriptionCodonPref.getFrequency()
returns a Distribution giving the frequency of codons (sums to one over the totality of codons).SimpleCodonPref.getFrequency()
CodonPref.getFrequencyForSynonyms
(Symbol residue) returns a Distribution giving the frequency of synonymous codons.SimpleCodonPref.getFrequencyForSynonyms
(Symbol residue) WobbleDistribution.getFrequencyOfNonWobbleBases()
returns the frequency with which synonymous codons start with a specified pair of bases.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 DistributionModifierConstructorDescriptionSimpleCodonPref
(String geneticCodeName, Distribution codonPref, String name)