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Packages that use Distribution | |
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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 |
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Subinterfaces of Distribution in org.biojava.bio.dist | |
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interface |
OrderNDistribution
Provides an N'th order distribution. |
Classes in org.biojava.bio.dist that implement Distribution | |
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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 | |
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static Distribution |
DistributionTools.average(Distribution[] dists)
Averages two or more distributions. |
static Distribution |
DistributionTools.countToDistribution(Count c)
Make a distribution from a count. |
Distribution |
OrderNDistributionFactory.createDistribution(Alphabet alpha)
Creates an OrderNDistribution of the appropriate type. |
Distribution |
DistributionFactory.createDistribution(Alphabet alpha)
Generate a new Distribution as requested. |
Distribution |
DistributionFactory.DefaultDistributionFactory.createDistribution(Alphabet alpha)
|
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 |
UniformDistribution.getNullModel()
|
Distribution |
TranslatedDistribution.getNullModel()
|
Distribution |
SimpleDistribution.getNullModel()
|
Distribution |
PairDistribution.getNullModel()
|
Distribution |
GapDistribution.getNullModel()
|
Distribution |
Distribution.getNullModel()
Retrieve the null model Distribution that this Distribution recognizes. |
Distribution |
AbstractOrderNDistribution.getNullModel()
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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(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 Distribution | |
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void |
SimpleDistributionTrainerContext.addCount(Distribution dist,
Symbol sym,
double times)
|
void |
DistributionTrainerContext.addCount(Distribution dist,
Symbol sym,
double times)
Registers that sym was counted in this state. |
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(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 |
SimpleDistributionTrainerContext.getCount(Distribution dist,
Symbol sym)
|
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. |
protected static Distribution |
PairDistribution.getNullModel(Distribution first,
Distribution second)
Get a uniform null model over a PairDistribution over [first,second]. |
DistributionTrainer |
SimpleDistributionTrainerContext.getTrainer(Distribution dist)
|
DistributionTrainer |
DistributionTrainerContext.getTrainer(Distribution dist)
Return the Distribution trainer object from the current context. |
static 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 |
SimpleDistributionTrainerContext.registerDistribution(Distribution dist)
|
void |
DistributionTrainerContext.registerDistribution(Distribution dist)
Register a distribution object with this context. |
void |
SimpleDistributionTrainerContext.registerTrainer(Distribution dist,
DistributionTrainer trainer)
|
void |
DistributionTrainerContext.registerTrainer(Distribution dist,
DistributionTrainer trainer)
Register a Distribution and an associated DistributionTrainer object. |
void |
OrderNDistribution.setDistribution(Symbol sym,
Distribution dist)
Set the distribution assocated with a symbol. |
void |
TranslatedDistribution.setNullModel(Distribution dist)
|
void |
PairDistribution.setNullModel(Distribution nullModel)
|
void |
GapDistribution.setNullModel(Distribution nullModel)
|
void |
Distribution.setNullModel(Distribution nullDist)
Set the null model Distribution that this Distribution recognizes. |
void |
AbstractDistribution.setNullModel(Distribution nullModel)
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protected void |
UniformDistribution.setNullModelImpl(Distribution nullModel)
Assign a background distribution. |
protected void |
SimpleDistribution.setNullModelImpl(Distribution nullModel)
|
void |
AbstractOrderNDistribution.setNullModelImpl(Distribution nullModel)
|
protected abstract void |
AbstractDistribution.setNullModelImpl(Distribution nullModel)
Implement this to set the null model. |
static 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 Distribution | |
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PairDistribution(Distribution first,
Distribution second)
Create a new PairDistribution that represents the product of two other distributions. |
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SimpleDistribution(Distribution dist)
make an instance of SimpleDistribution with weights identical to the specified Distribution. |
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SimpleDistributionTrainer(Distribution dis)
Deprecated. |
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TranslatedDistribution(ReversibleTranslationTable table,
Distribution other,
DistributionFactory distFact)
Create a new TranslatedDistribution. |
Uses of Distribution in org.biojava.bio.dp |
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Methods in org.biojava.bio.dp that return Distribution | |
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Distribution |
WeightMatrix.getColumn(int column)
Retrieve a column as an EmissionState. |
Distribution |
SimpleWeightMatrix.getColumn(int column)
|
Distribution |
SimpleEmissionState.getDistribution()
|
Distribution |
EmissionState.getDistribution()
Get the Distribution associated with this state. |
Distribution |
WMAsMM.getWeights(State source)
|
Distribution |
SimpleMarkovModel.getWeights(State source)
|
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 | |
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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 |
WMAsMM.setWeights(State source,
Distribution dist)
|
void |
SimpleMarkovModel.setWeights(State source,
Distribution dist)
Use this methods to customize the transition probabilities. |
void |
MarkovModel.setWeights(State source,
Distribution dist)
Set the probability distribution over the transitions from 'source'. |
Constructors in org.biojava.bio.dp with parameters of type Distribution | |
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SimpleEmissionState(String name,
Annotation ann,
int[] advance,
Distribution dis)
|
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SimpleWeightMatrix(Distribution[] columns)
|
Uses of Distribution in org.biojava.bio.gui |
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Methods in org.biojava.bio.gui that return Distribution | |
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Distribution |
LogoContext.getDistribution()
|
Distribution |
DistributionLogo.getDistribution()
Retrieve the currently rendered dist. |
Methods in org.biojava.bio.gui with parameters of type Distribution | |
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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 |
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Methods in org.biojava.bio.molbio that return Distribution | |
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Distribution |
Composition.getDistribution()
Returns the distribution backing this class. |
Uses of Distribution in org.biojava.bio.program.hmmer |
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Methods in org.biojava.bio.program.hmmer with parameters of type Distribution | |
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protected 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 Distribution | |
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ProfileEmissionState(String str,
Annotation ann,
int[] adv,
Distribution dis)
|
Uses of Distribution in org.biojava.bio.program.phred |
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Methods in org.biojava.bio.program.phred that return Distribution | |
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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 |
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Methods in org.biojava.bio.seq that return Distribution | |
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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 |
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Methods in org.biojava.bio.symbol that return Distribution | |
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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 | |
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SimpleCodonPref(String geneticCodeName,
Distribution codonPref,
String name)
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