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 OrderNDistribution.getDistribution(Symbol sym)
           
 Distribution UniformDistribution.getNullModel()
           
 Distribution OrderNDistributionFactory.createDistribution(Alphabet alpha)
          Creates an OrderNDistribution of the appropriate type
 Distribution TranslatedDistribution.getNullModel()
           
 Distribution SimpleDistribution.getNullModel()
           
 Distribution XMLDistributionReader.parseXML(java.io.InputStream is)
          Reads an XML representation of a Distribution from a file
 Distribution AbstractOrderNDistribution.getNullModel()
           
protected static Distribution PairDistribution.getNullModel(Distribution first, Distribution second)
           
 Distribution PairDistribution.getNullModel()
           
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 Distribution.getNullModel()
          Retrieve the null model Distribution that this Distribution recognizes.
 Distribution GapDistribution.getNullModel()
           
 Distribution DistributionFactory.createDistribution(Alphabet alpha)
          Generate a new Distribution as requested.
 Distribution DistributionFactory.DefaultDistributionFactory.createDistribution(Alphabet alpha)
           
 

Methods in org.biojava.bio.dist with parameters of type Distribution
 void OrderNDistribution.setDistribution(Symbol sym, Distribution dist)
           
protected  void UniformDistribution.setNullModelImpl(Distribution nullModel)
          Assign a background distribution
 void TranslatedDistribution.setNullModel(Distribution dist)
           
protected  void SimpleDistribution.setNullModelImpl(Distribution nullModel)
           
 void AbstractOrderNDistribution.setNullModelImpl(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)
           
protected abstract  void AbstractDistribution.setNullModelImpl(Distribution nullModel)
           
 void AbstractDistribution.setNullModel(Distribution nullModel)
           
protected static Distribution PairDistribution.getNullModel(Distribution first, Distribution second)
           
 void PairDistribution.setNullModel(Distribution nullModel)
           
 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.
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 Distribution.setNullModel(Distribution nullDist)
          Set the null model Distribution that this Distribution recognizes.
 void GapDistribution.setNullModel(Distribution nullModel)
           
 void XMLDistributionWriter.writeDistribution(Distribution d, java.io.OutputStream os)
          Writes an OrderNDistribution or simple Distribution to an XML file.
 

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

Uses of Distribution in org.biojava.bio.dp
 

Methods in org.biojava.bio.dp that return Distribution
 Distribution MarkovModel.getWeights(State source)
          Get a probability Distribution over the transition from 'source'.
 Distribution SimpleMarkovModel.getWeights(State source)
           
 Distribution EmissionState.getDistribution()
           Get the Distribution associated with this state.
 Distribution SimpleEmissionState.getDistribution()
           
 Distribution WeightMatrix.getColumn(int column)
          Retrieve a column as an EmissionState.
 Distribution SimpleWeightMatrix.getColumn(int column)
           
 Distribution WMAsMM.getWeights(State source)
           
 

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

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 LogoContext.getDistribution()
           
 Distribution DistributionLogo.getDistribution()
          Retrieve the currently rendered dist.
 

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.