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 
 

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

Methods in org.biojava.bio.dist with parameters of type Distribution
 void TranslatedDistribution.setNullModel(Distribution dist)
           
 void GapDistribution.setNullModel(Distribution nullModel)
           
 void SimpleDistributionTrainerContext.registerDistribution(Distribution dist)
           
 void SimpleDistributionTrainerContext.registerTrainer(Distribution dist, DistributionTrainer trainer)
           
 DistributionTrainer SimpleDistributionTrainerContext.getTrainer(Distribution dist)
           
 void SimpleDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times)
           
 double SimpleDistributionTrainerContext.getCount(Distribution dist, Symbol sym)
           
 void OrderNDistribution.setDistribution(Symbol sym, Distribution dist)
           
static void DistributionTools.writeToXML(Distribution d, java.io.OutputStream os)
          Writes a Distribution to XML that can be read with the readFromXML method.
static void DistributionTools.randomizeDistribution(Distribution d)
          Randomizes the weights of a Distribution
static boolean DistributionTools.areEmissionSpectraEqual(Distribution a, Distribution b)
          Compares the emission spectra of two distributions
static boolean DistributionTools.areEmissionSpectraEqual(Distribution[] a, Distribution[] b)
          Compares the emission spectra of two distribution arrays
static java.util.HashMap DistributionTools.KLDistance(Distribution observed, Distribution expected, double logBase)
          A method to calculate the Kullback-Liebler Distance (relative entropy)
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.
static double DistributionTools.bitsOfInformation(Distribution observed)
          Calculates the total bits of information for a distribution.
static Distribution DistributionTools.average(Distribution[] dists)
          Averages two or more distributions.
static Sequence DistributionTools.generateSequence(java.lang.String name, Distribution d, int length)
          Produces a sequence by randomly sampling the Distribution
 void DistributionTrainerContext.registerDistribution(Distribution dist)
           Register a distribution object with this context.
 void DistributionTrainerContext.registerTrainer(Distribution dist, DistributionTrainer trainer)
           Register a Distribution and an associated DistributionTrainer object.
 DistributionTrainer DistributionTrainerContext.getTrainer(Distribution dist)
          Return the Distribution trainer object from the current context.
 void DistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times)
           Registers that sym was counted in this state.
 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.
 void AbstractOrderNDistribution.setNullModelImpl(Distribution nullModel)
           
 void XMLDistributionWriter.writeDistribution(Distribution d, java.io.OutputStream os)
          Writes an OrderNDistribution or simple Distribution to an XML file.
protected  void SimpleDistribution.setNullModelImpl(Distribution nullModel)
           
protected  void UniformDistribution.setNullModelImpl(Distribution nullModel)
          Assign a background distribution
protected static Distribution PairDistribution.getNullModel(Distribution first, Distribution second)
           
 void PairDistribution.setNullModel(Distribution nullModel)
           
protected abstract  void AbstractDistribution.setNullModelImpl(Distribution nullModel)
           
 void AbstractDistribution.setNullModel(Distribution nullModel)
           
 void Distribution.setNullModel(Distribution nullDist)
          Set the null model Distribution that this Distribution recognizes.
 

Constructors in org.biojava.bio.dist with parameters of type Distribution
TranslatedDistribution(ReversibleTranslationTable table, Distribution other, DistributionFactory distFact)
          Users should make these thigs via getDistribuiton.
SimpleDistributionTrainer(Distribution dis)
           
PairDistribution(Distribution first, Distribution second)
           
 

Uses of Distribution in org.biojava.bio.dp
 

Methods in org.biojava.bio.dp that return Distribution
 Distribution SimpleEmissionState.getDistribution()
           
 Distribution WeightMatrix.getColumn(int column)
          Retrieve a column as an EmissionState.
 Distribution EmissionState.getDistribution()
           Get the Distribution associated with this state.
 Distribution SimpleMarkovModel.getWeights(State source)
           
 Distribution WMAsMM.getWeights(State source)
           
 Distribution SimpleWeightMatrix.getColumn(int column)
           
 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
 void SimpleEmissionState.setDistribution(Distribution dis)
           
 void EmissionState.setDistribution(Distribution dis)
          Set the Distribution associated with this state.
 void SimpleMarkovModel.setWeights(State source, Distribution dist)
          Use this methods to customize the transition probabilities.
 void WMAsMM.setWeights(State source, Distribution dist)
           
 void MarkovModel.setWeights(State source, Distribution dist)
          Set the probability distribution over the transitions from 'source'.
 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)
           
 

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
 void DistributionLogo.setDistribution(Distribution dist)
           Set the dist to render.
static double DistributionLogo.entropy(Distribution dist, Symbol s)
          Calculate the information content of a symbol in bits.
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(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.phredToDistArray(PhredSequence s)
          Converts a Phred sequence to an array of distributions.
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.