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.molbio The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR. 
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 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 Distribution.getNullModel()
          Retrieve the null model Distribution that this Distribution recognizes.
 Distribution PairDistribution.getNullModel()
           
 Distribution UniformDistribution.getNullModel()
           
 Distribution TranslatedDistribution.getNullModel()
           
 Distribution SimpleDistribution.getNullModel()
           
 Distribution GapDistribution.getNullModel()
           
 Distribution AbstractOrderNDistribution.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(java.io.InputStream is)
          Reads an XML representation of a Distribution from a file.
static Distribution DistributionTools.readFromXML(java.io.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(java.lang.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 java.util.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 Distribution.setNullModel(Distribution nullDist)
          Set the null model Distribution that this Distribution recognizes.
 void PairDistribution.setNullModel(Distribution nullModel)
           
 void TranslatedDistribution.setNullModel(Distribution dist)
           
 void GapDistribution.setNullModel(Distribution nullModel)
           
 void AbstractDistribution.setNullModel(Distribution nullModel)
           
protected  void UniformDistribution.setNullModelImpl(Distribution nullModel)
          Assign a background distribution.
protected  void SimpleDistribution.setNullModelImpl(Distribution nullModel)
           
protected abstract  void AbstractDistribution.setNullModelImpl(Distribution nullModel)
          Implement this to set the null model.
 void AbstractOrderNDistribution.setNullModelImpl(Distribution nullModel)
           
static java.util.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, java.io.OutputStream os)
          Writes an OrderNDistribution or simple Distribution to an XML file.
static void DistributionTools.writeToXML(Distribution d, java.io.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 MarkovModel.getWeights(State source)
          Get a probability Distribution over the transition from 'source'.
 Distribution WMAsMM.getWeights(State source)
           
 Distribution SimpleMarkovModel.getWeights(State 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 MarkovModel.setWeights(State source, Distribution dist)
          Set the probability distribution over the transitions from 'source'.
 void WMAsMM.setWeights(State source, Distribution dist)
           
 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
SimpleEmissionState(java.lang.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.molbio
 

Methods in org.biojava.bio.molbio that return Distribution
 Distribution Composition.getDistribution()
          Returns the distribution backing this class.
 

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(java.lang.String str, Annotation ann, int[] adv, Distribution dis)
           
protected  EmissionState HmmerProfileHMM.makeNewMatchState(java.lang.String str, Annotation ann, int[] adv, Distribution dis)
           
 

Constructors in org.biojava.bio.program.hmmer with parameters of type Distribution
ProfileEmissionState(java.lang.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 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
SimpleCodonPref(java.lang.String geneticCodeName, Distribution codonPref, java.lang.String name)