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.
-
Uses of Distribution in org.biojava.bio.dist
Subinterfaces of Distribution in org.biojava.bio.distModifier and TypeInterfaceDescriptioninterfaceProvides an N'th order distribution.Classes in org.biojava.bio.dist that implement DistributionModifier and TypeClassDescriptionclassAn abstract implementation of Distribution.classSimple base class for OrderNDistributions.classThis distribution emits gap symbols.classClass for pairing up two independant distributions.classA simple implementation of a distribution, which works with any finite alphabet.classA translated view of some underlying distribution.classAn implementation of an uniform distributionclassA distribution which does not interact with the training framework.Methods in org.biojava.bio.dist that return DistributionModifier and TypeMethodDescriptionstatic final DistributionDistributionTools.average(Distribution[] dists) Averages two or more distributions.static DistributionDistributionTools.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 DistributionPairDistribution.getNullModel(Distribution first, Distribution second) Get a uniform null model over a PairDistribution over [first,second].SimpleDistribution.getNullModel()TranslatedDistribution.getNullModel()UniformDistribution.getNullModel()static final DistributionDistributionTools.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 DistributionDistributionTools.readFromXML(InputStream is) Read a distribution from XML.Methods in org.biojava.bio.dist with parameters of type DistributionModifier and TypeMethodDescriptionvoidDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times) Registers that sym was counted in this state.voidSimpleDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times) static final booleanDistributionTools.areEmissionSpectraEqual(Distribution[] a, Distribution[] b) Compares the emission spectra of two distribution arrays.static final booleanDistributionTools.areEmissionSpectraEqual(Distribution a, Distribution b) Compares the emission spectra of two distributions.static final DistributionDistributionTools.average(Distribution[] dists) Averages two or more distributions.static final doubleDistributionTools.bitsOfInformation(Distribution observed) Calculates the total bits of information for a distribution.static final SequenceDistributionTools.generateSequence(String name, Distribution d, int length) Produces a sequence by randomly sampling the Distribution.static final SymbolListDistributionTools.generateSymbolList(Distribution d, int length) Produces aSymbolListby randomly sampling a Distribution.doubleDistributionTrainerContext.getCount(Distribution dist, Symbol sym) Return the number of counts of a particular symbol which will be used to train the specified distribution.doubleSimpleDistributionTrainerContext.getCount(Distribution dist, Symbol sym) protected static DistributionPairDistribution.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 HashMapDistributionTools.KLDistance(Distribution observed, Distribution expected, double logBase) A method to calculate the Kullback-Liebler Distance (relative entropy).static voidDistributionTools.randomizeDistribution(Distribution d) Randomizes the weights of aDistribution.voidDistributionTrainerContext.registerDistribution(Distribution dist) Register a distribution object with this context.voidSimpleDistributionTrainerContext.registerDistribution(Distribution dist) voidDistributionTrainerContext.registerTrainer(Distribution dist, DistributionTrainer trainer) Register a Distribution and an associated DistributionTrainer object.voidSimpleDistributionTrainerContext.registerTrainer(Distribution dist, DistributionTrainer trainer) voidOrderNDistribution.setDistribution(Symbol sym, Distribution dist) Set the distribution assocated with a symbol.final voidAbstractDistribution.setNullModel(Distribution nullModel) voidDistribution.setNullModel(Distribution nullDist) Set the null model Distribution that this Distribution recognizes.voidGapDistribution.setNullModel(Distribution nullModel) voidPairDistribution.setNullModel(Distribution nullModel) voidTranslatedDistribution.setNullModel(Distribution dist) protected abstract voidAbstractDistribution.setNullModelImpl(Distribution nullModel) Implement this to set the null model.voidAbstractOrderNDistribution.setNullModelImpl(Distribution nullModel) protected voidSimpleDistribution.setNullModelImpl(Distribution nullModel) protected voidUniformDistribution.setNullModelImpl(Distribution nullModel) Assign a background distribution.static final HashMapDistributionTools.shannonEntropy(Distribution observed, double logBase) A method to calculate the Shannon Entropy for a Distribution.static doubleDistributionTools.totalEntropy(Distribution observed) Calculates the total Entropy for a Distribution.voidXMLDistributionWriter.writeDistribution(Distribution d, OutputStream os) Writes an OrderNDistribution or simple Distribution to an XML file.static voidDistributionTools.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 DistributionSimpleEmissionState.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 TypeMethodDescriptiondoubleScoreType.calculateScore(Distribution dist, Symbol sym) Calculates the score associated with a distribution and a symbol.doubleScoreType.NullModel.calculateScore(Distribution dist, Symbol sym) doubleScoreType.Odds.calculateScore(Distribution dist, Symbol sym) doubleScoreType.Probability.calculateScore(Distribution dist, Symbol sym) voidEmissionState.setDistribution(Distribution dis) Set the Distribution associated with this state.final voidSimpleEmissionState.setDistribution(Distribution dis) voidMarkovModel.setWeights(State source, Distribution dist) Set the probability distribution over the transitions from 'source'.voidSimpleMarkovModel.setWeights(State source, Distribution dist) Use this methods to customize the transition probabilities.voidWMAsMM.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 doubleDistributionLogo.entropy(Distribution dist, Symbol s) Calculate the information content of a symbol in bits.voidDistributionLogo.setDistribution(Distribution dist) Set the dist to render.static doubleDistributionLogo.totalBits(Distribution dist) Retrieve the maximal number of bits possible for this type of dist.static doubleDistributionLogo.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 symbolDistributions 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 EmissionStateHmmerProfileHMM.makeNewInsertState(String str, Annotation ann, int[] adv, Distribution dis) protected EmissionStateHmmerProfileHMM.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 DistributionDNATools.getDNADistribution(double fractionGC) return a SimpleDistribution of specified GC content.static DistributionDNATools.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)