A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

a - Variable in class alun.gchap.Genotype

The first allele index.

a1 - Variable in class alun.genio.NumberedAllelePhenotype

The first allele at this locus for the individual whose data this is.

a2 - Variable in class alun.genio.NumberedAllelePhenotype

The second allele at this locus for the individual whose data this is.

AbstractGraph<V> - Class in alun.graph

AbstractGraph() - Constructor for class alun.graph.AbstractGraph

AbstractMappable - Class in alun.viewgraph

An abstract class that defines what is needed of an object in order to be able to set coordinates and draw it.

AbstractMappable() - Constructor for class alun.viewgraph.AbstractMappable

accept() - Method in class alun.mcld.DecomposableSearch

accept() - Method in interface alun.mcld.GraphMHScheme

accept() - Method in class alun.mcld.IntervalSearch

actionPerformed(ActionEvent) - Method in class alun.view.OutputFileListener

ActiveCanvas - Class in alun.view

ActiveCanvas(Paintable) - Constructor for class alun.view.ActiveCanvas

add(V) - Method in class alun.graph.AbstractGraph

add(K) - Method in class alun.graph.MapAsCollection

add(V) - Method in class alun.graph.MaskedNetwork

add(V) - Method in interface alun.graph.MutableGraph

add(Function) - Method in class alun.markov.Product

add(Collection<Function>) - Method in class alun.markov.Product

add(Function) - Method in class alun.mcld.LDModel

add(LogLikelihood) - Method in class alun.mcld.LogLikelihood

add(V) - Method in class alun.util.IntervalTree

add(E) - Method in class alun.util.RadixPlaneSorter

addAll(Collection<? extends K>) - Method in class alun.graph.MapAsCollection

addAll() - Method in class alun.viewgraph.EditingCoordinator

addComponent(MutableGraph<? super V>, V, Graph<V>) - Static method in class alun.graph.GraphFunction

addInducedSubgraph(MutableGraph<? super V>, Collection<V>, Graph<V>) - Static method in class alun.graph.GraphFunction

addInducedSubgraph(MutableEdgedGraph<? super V, ? super E>, Collection<V>, EdgedGraph<V, E>) - Static method in class alun.graph.GraphFunction

addKid(Object) - Method in class alun.genio.Family

addObservations(int, int, int) - Method in class alun.gchap.Marker

Adds a count for the given observation to the trait.

addProduct(Product) - Method in class alun.markov.Product

addRemoveAnalysis(PrintWriter) - Method in class alun.mcld.JointScheme

addTriplet(Triplet) - Method in class alun.genio.Pedigree

addTriplet(Triplet[]) - Method in class alun.genio.Pedigree

adjustmentValueChanged(AdjustmentEvent) - Method in class alun.view.ScrollWidget

AFFECTION_STATUS - Static variable in class alun.genio.LinkageLocus

Represents the linakge affectation status locus type.

AffectionStatusLocus - Class in alun.genio

This class represents a locus as specified in the linkage affectation status format.

AffectionStatusLocus(LinkageFormatter) - Constructor for class alun.genio.AffectionStatusLocus

Creates a new locus with data read from the given input formatter.

AffectionStatusLocus(AffectionStatusLocus) - Constructor for class alun.genio.AffectionStatusLocus

AffectionStatusPhenotype - Class in alun.genio

This represents the data for an individual at a locus specified in the linkage affected status format.

AffectionStatusPhenotype(AffectionStatusLocus, int, int) - Constructor for class alun.genio.AffectionStatusPhenotype

Creates a new phenotype from the given status and liability class numbers.

Allele - Class in alun.genepi

Allele(int) - Constructor for class alun.genepi.Allele

AlleleErrorPenetrance - Class in alun.genepi

AlleleErrorPenetrance(Allele, Allele, Error, double[][]) - Constructor for class alun.genepi.AlleleErrorPenetrance

alleleFreqs(int) - Method in interface alun.genio.GeneticDataSource

The frequencies of the alleles at the jth genetic locus.

alleleFreqs(int) - Method in class alun.genio.LinkageInterface

alleleFrequencies() - Method in class alun.gchap.Locus

Returns the frequencies of the alleles at the locus.

alleleFrequencies() - Method in class alun.genio.LinkageLocus

Returns the allele frequencies for the locus.

alleleNames() - Method in class alun.gchap.Locus

Returns the names of the alleles at the locus.

AllelePenetrance - Class in alun.genepi

AllelePenetrance(Allele, Allele, double[][]) - Constructor for class alun.genepi.AllelePenetrance

AllelePrior - Class in alun.genepi

AllelePrior(Allele, double[]) - Constructor for class alun.genepi.AllelePrior

AllelesToGenotype - Class in alun.mcld

AllelesToGenotype(Allele, Allele, Genotype) - Constructor for class alun.mcld.AllelesToGenotype

allocateInvolTables() - Method in class alun.genepi.GenotypeModel

allocateInvolTables() - Method in class alun.markov.DenseGraphicalModel

allocateInvolTables() - Method in class alun.markov.GraphicalModel

allocateOutputTables() - Method in class alun.genepi.GenotypeModel

allocateOutputTables() - Method in class alun.markov.DenseGraphicalModel

allocateOutputTables() - Method in class alun.markov.GraphicalModel

alun.gchap - package alun.gchap

alun.genepi - package alun.genepi

alun.genio - package alun.genio

alun.graph - package alun.graph

alun.markov - package alun.markov

alun.mcld - package alun.mcld

alun.util - package alun.util

alun.view - package alun.view

alun.viewgraph - package alun.viewgraph

AnnealMover - Class in alun.mcld

AnnealMover() - Constructor for class alun.mcld.AnnealMover

ApproxGCHap - Class in alun.gchap

This class contains a main method for running the approximate equivalent of GCHap.

ApproxGCHap() - Constructor for class alun.gchap.ApproxGCHap

ApproxGCHap - Class in <Unnamed>

This program finds approximations to the maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals.

ApproxGCHap() - Constructor for class ApproxGCHap

Arrow - Class in alun.viewgraph

Arrow(Mappable, Mappable) - Constructor for class alun.viewgraph.Arrow

asArray() - Method in class alun.genio.IntArray

asArray() - Method in class alun.util.IntArray

AuxiliaryFunction - Class in alun.genepi

AuxiliaryFunction() - Constructor for class alun.genepi.AuxiliaryFunction

AuxiliaryModel - Class in alun.genepi

AuxiliaryModel(Product) - Constructor for class alun.genepi.AuxiliaryModel

AuxiliaryVariable - Class in alun.genepi

AuxiliaryVariable(int, LocusVariables) - Constructor for class alun.genepi.AuxiliaryVariable

AuxiliaryVariableClique - Class in alun.genepi

AuxiliaryVariableClique(Set<Variable>, Clique) - Constructor for class alun.genepi.AuxiliaryVariableClique

AuxLinkFunction - Class in alun.genepi

AuxLinkFunction(AuxiliaryVariable, AuxiliaryVariable, double, double) - Constructor for class alun.genepi.AuxLinkFunction

AuxLocusFunction - Class in alun.genepi

AuxLocusFunction(AuxiliaryVariable) - Constructor for class alun.genepi.AuxLocusFunction

AuxOneGenVariable - Class in alun.genepi

AuxOneGenVariable(Inheritance, Inheritance, LocusVariables) - Constructor for class alun.genepi.AuxOneGenVariable

AuxOneGenVariable(Set<Inheritance>, Set<Inheritance>, LocusVariables) - Constructor for class alun.genepi.AuxOneGenVariable

AuxThreeGenVariable - Class in alun.genepi

AuxThreeGenVariable(Set<Inheritance>, Set<Inheritance>, Set<Inheritance>, Set<Inheritance>, LocusVariables) - Constructor for class alun.genepi.AuxThreeGenVariable

B

b - Variable in class alun.gchap.Genotype

The second allele index.

BasicClique - Class in alun.markov

BasicClique(Set<Variable>, Clique) - Constructor for class alun.markov.BasicClique

BasicVariable - Class in alun.markov

BasicVariable(int) - Constructor for class alun.markov.BasicVariable

BINARY_FACTORS - Static variable in class alun.genio.LinkageLocus

Represents the linkage binary factors locus type.

BnBForLD - Class in alun.mcld

BnBForLD(LDModel, double) - Constructor for class alun.mcld.BnBForLD

BufferedCanvas - Class in alun.view

BufferedCanvas(Paintable) - Constructor for class alun.view.BufferedCanvas

C

calc(Graph<Locus>) - Method in class alun.mcld.LikelihoodCalculator

call(int, int) - Method in interface alun.genio.GeneticDataSource

Returns a string representation of the observation for the ith individuals at the jth locus.

call(int, int) - Method in class alun.genio.LinkageInterface

canonicalOrder() - Method in class alun.genio.LinkageInterface

CartesianPoint - Interface in alun.util

CheckErrors - Class in <Unnamed>

This program finds the posterior probabilities of errors for genotypes on individuals in pedigrees given a set of observed genotypes and the pedigree structure.

CheckErrors() - Constructor for class CheckErrors

CheckFormat - Class in <Unnamed>

This program reads in LINKAGE paramter and pedigree files, checks that they are readable and then outputs the checked files.

CheckFormat() - Constructor for class CheckFormat

className - Static variable in class alun.view.ViewingApplet

clear() - Method in class alun.graph.AbstractGraph

clear() - Method in class alun.graph.MapAsCollection

clear() - Method in class alun.graph.MaskedNetwork

clear() - Method in interface alun.graph.MutableGraph

clear() - Method in class alun.mcld.LikelihoodCalculator

clear() - Method in class alun.util.HashOfHash

Empties the current structure.

clearInvolTables() - Method in class alun.markov.GraphicalModel

clearOutputTables() - Method in class alun.markov.GraphicalModel

Clique - Class in alun.markov

Clique(Set<Variable>, Clique) - Constructor for class alun.markov.Clique

cMToMb(double) - Static method in class alun.genio.LinkageParameterData

Converts centiMorgans to Megabases at 1 to 1.

cMToTheta(double) - Static method in class alun.genio.LinkageParameterData

Converts centiMorgans to recombination fractions using the Kosambi conversion.

collect() - Method in class alun.markov.BasicClique

collect() - Method in class alun.markov.Clique

collect() - Method in class alun.markov.GraphicalModel

comment - Variable in class alun.genio.AffectionStatusLocus

An array holding the comment strings for each linkage liability class.

comment - Variable in class alun.genio.LinkageIndividual

A string representing anything that was left on this individual's input line after all thee pedigree, sex, proband and locus informatio was read in.

comment - Variable in class alun.genio.QuantitativeLocus

compareTo(DoubleValue) - Method in class alun.util.DoubleValue

compareTo(IntValue) - Method in class alun.util.IntValue

completeProduct() - Method in class alun.genepi.LinkageVariables

completeProduct(int) - Method in class alun.genepi.LinkageVariables

CompoundVariable - Class in alun.markov

compute(Table[]) - Method in class alun.genepi.AuxiliaryVariableClique

compute(Table[]) - Method in class alun.genepi.TripletClique

compute(Table[]) - Method in class alun.markov.BasicClique

connect(V, V) - Method in class alun.graph.AbstractGraph

connect(V, V, E) - Method in class alun.graph.EdgedNetwork

connect(V, V) - Method in class alun.graph.MaskedNetwork

connect(V, V, E) - Method in class alun.graph.MaskedNetwork

connect(V, V, E) - Method in interface alun.graph.MutableEdgedGraph

connect(V, V) - Method in interface alun.graph.MutableGraph

connectedLocusProduct(int) - Method in class alun.genepi.LinkageVariables

connectedLocusProduct(int, boolean, boolean) - Method in class alun.genepi.LinkageVariables

connection(Object, Object) - Method in interface alun.graph.EdgedGraph

connection(Object, Object) - Method in class alun.graph.EdgedNetwork

connection(Object, Object) - Method in class alun.graph.MaskedNetwork

connects(Object, Object) - Method in class alun.graph.AbstractGraph

connects(Object, Object) - Method in interface alun.graph.Graph

connects(Object, Object) - Method in class alun.graph.MaskedNetwork

connects(Object, Object) - Method in class alun.markov.Product

connects(Object, Object) - Method in class alun.util.IntervalTreeGraph

contains(Object) - Method in class alun.graph.AbstractGraph

contains(Object) - Method in interface alun.graph.Graph

contains(Object) - Method in class alun.graph.MapAsCollection

contains(Object) - Method in class alun.graph.MaskedNetwork

contains(Object) - Method in class alun.markov.Product

contains(Object) - Method in class alun.util.IntervalTree

contains(double, double) - Method in class alun.viewgraph.AbstractMappable

Returns true iff the given point is contained in the drawn image of the object.

contains(double, double) - Method in class alun.viewgraph.LabelledBlob

contains(double, double) - Method in interface alun.viewgraph.Mappable

containsAll(Collection<?>) - Method in class alun.graph.MapAsCollection

countAlleleFreqs(int) - Method in class alun.genio.LinkageDataSet

countAlleleFreqs() - Method in class alun.genio.LinkageDataSet

covar - Variable in class alun.genio.QuantitativeLocus

crash(String) - Method in class alun.genio.LinkageFormatter

Curve - Interface in alun.util

cutset() - Method in class alun.markov.Clique

D

DagMover - Class in alun.viewgraph

DagMover() - Constructor for class alun.viewgraph.DagMover

DecomposableSearch - Class in alun.mcld

DecomposableSearch(Collection<Locus>) - Constructor for class alun.mcld.DecomposableSearch

Decomposition<V> - Class in alun.graph

A Decomposition is a directed graph of sets of vertices of a given graph.

Decomposition(Graph<V>, Collection<V>) - Constructor for class alun.graph.Decomposition

Decomposition(Graph<V>) - Constructor for class alun.graph.Decomposition

defvalue - Static variable in class alun.viewgraph.LocalMover

DenseGraphicalModel - Class in alun.markov

DenseGraphicalModel(Product) - Constructor for class alun.markov.DenseGraphicalModel

DenseGraphicalModel(Product, Variable) - Constructor for class alun.markov.DenseGraphicalModel

DenseGraphicalModel(Product, Collection<Variable>) - Constructor for class alun.markov.DenseGraphicalModel

DenseTable - Class in alun.markov

An implementation of the Table interface that stores the values in an array of doubles.

DenseTable(Collection<? extends Variable>, double[]) - Constructor for class alun.markov.DenseTable

DenseTable(Collection<? extends Variable>) - Constructor for class alun.markov.DenseTable

densityOf(double[]) - Method in class alun.genio.QuantitativeLocus

destroy() - Method in class alun.view.ViewingApplet

determinant - Variable in class alun.genio.QuantitativeLocus

df() - Method in class alun.mcld.LogLikelihood

DIAMOND - Static variable in class alun.viewgraph.LabelledBlob

DiploGUI - Class in alun.mcld

DiploGUI(JointScheme) - Constructor for class alun.mcld.DiploGUI

Diplotypes - Class in alun.mcld

Diplotypes(GeneticDataSource, double) - Constructor for class alun.mcld.Diplotypes

Diplotypes(GeneticDataSource, double, int) - Constructor for class alun.mcld.Diplotypes

DirectedGraph<E> - Interface in alun.graph

DirectedNetwork<V> - Class in alun.graph

DirectedNetwork() - Constructor for class alun.graph.DirectedNetwork

disconnect(Object, Object) - Method in class alun.graph.AbstractGraph

disconnect(Object, Object) - Method in class alun.graph.MaskedNetwork

disconnect(Object, Object) - Method in interface alun.graph.MutableGraph

disequilibrium - Variable in class alun.genio.LinkageParameterData

distances - Variable in class alun.genio.LinkageParameterData

distribute() - Method in class alun.markov.BasicClique

distribute() - Method in class alun.markov.Clique

distributeCount(double[]) - Method in class alun.gchap.Phenotype

Distributes the count for this phenotype to the alleles that are involved in geneotype that can give rise to the phenotype.

DoubleValue - Class in alun.util

A wrapper around a modifiable double.

DoubleValue() - Constructor for class alun.util.DoubleValue

DoubleValue(double) - Constructor for class alun.util.DoubleValue

downCode() - Method in class alun.gchap.GeneticTrait

Removes from the locus any alleles that have zero frequency.

downCode(double) - Method in class alun.gchap.GeneticTrait

downCode(boolean) - Method in class alun.genio.LinkageDataSet

downCode(int) - Method in class alun.genio.LinkageDataSet

DownCodeAlleles - Class in <Unnamed>

This program reduces the number of alleles in the models for the given genetic loci to include only alleles that appear in the pedigree file plus one catchall unseen alleles that has the total frequency of the original unseen alleles.

DownCodeAlleles() - Constructor for class DownCodeAlleles

drop() - Method in class alun.genepi.AuxiliaryVariableClique

drop() - Method in class alun.markov.BasicClique

drop() - Method in class alun.markov.Clique

drop() - Method in class alun.markov.GraphicalModel

Dummy - Class in <Unnamed>

Dummy() - Constructor for class Dummy

DynamicMap<V> - Class in alun.viewgraph

DynamicMap(Graph<V>) - Constructor for class alun.viewgraph.DynamicMap

DynamicMappableMap<V extends Mappable> - Class in alun.viewgraph

DynamicMappableMap(Graph<? extends V>) - Constructor for class alun.viewgraph.DynamicMappableMap

E

EdgedDirectedNetwork<V,E> - Class in alun.graph

EdgedDirectedNetwork() - Constructor for class alun.graph.EdgedDirectedNetwork

EdgedGraph<V,E> - Interface in alun.graph

EdgedNetwork<V,E> - Class in alun.graph

EdgedNetwork() - Constructor for class alun.graph.EdgedNetwork

EdgedNetwork(EdgedGraph<? extends V, ? extends E>) - Constructor for class alun.graph.EdgedNetwork

EditingCoordinator - Class in alun.viewgraph

EditingCoordinator(MapEditor) - Constructor for class alun.viewgraph.EditingCoordinator

EditingMouser - Class in alun.viewgraph

EditingMouser(MapViewer) - Constructor for class alun.viewgraph.EditingMouser

equals(Object) - Method in class alun.genio.IntArray

equals(Object) - Method in class alun.util.DoubleValue

equals(Object) - Method in class alun.util.IntArray

equals(Object) - Method in class alun.util.IntValue

Error - Class in alun.genepi

Error() - Constructor for class alun.genepi.Error

error(int) - Method in class alun.genepi.LocusVariables

ErrorPenetrance - Class in alun.genepi

ErrorPenetrance(Genotype, Error, double[][]) - Constructor for class alun.genepi.ErrorPenetrance

ErrorPrior - Class in alun.genepi

ErrorPrior(Error, double) - Constructor for class alun.genepi.ErrorPrior

errors() - Method in class alun.genepi.LocusVariables

expand(Mappable) - Method in class alun.viewgraph.EditingCoordinator

expandComponent(Mappable) - Method in class alun.viewgraph.EditingCoordinator

expectedFrequency() - Method in class alun.gchap.Phenotype

Returns the expected frequency of the phenotype derived from the current allele frequencies.

ExtendedLMSampler - Class in alun.genepi

ExtendedLMSampler(LinkageVariables) - Constructor for class alun.genepi.ExtendedLMSampler

ExtendedLMSampler(LinkageVariables, int[]) - Constructor for class alun.genepi.ExtendedLMSampler

F

f(double) - Method in class alun.genepi.MaxLoder

f(double) - Method in interface alun.util.Curve

Family - Class in alun.genio

Family() - Constructor for class alun.genio.Family

familyMeiosisProduct(int) - Method in class alun.genepi.LinkageVariables

female(Object) - Method in class alun.genio.MarriageNodeMap

fillIn(Variable, Variable) - Method in class alun.markov.Product

find(String) - Method in class alun.viewgraph.EditingCoordinator

FindErrorProbs - Class in alun.genepi

FindErrorProbs() - Constructor for class alun.genepi.FindErrorProbs

findMarginals() - Method in class alun.markov.GraphicalModel

findPhenotype(int, int) - Method in class alun.gchap.Marker

Returns the phenotype for the given pair of alleles.

findPhenotype(Phenotype, Phenotype) - Method in class alun.gchap.MultiLocusTrait

Returns the phenotype of the multilocus trait that represents the same information as those specified for the two constituent traits.

findPhenotype(String) - Method in class alun.gchap.SNP

Finds the phenotype corresponding to the given string.

firstbornid - Variable in class alun.genio.LinkageIndividual

The individual's first born child's id number.

firstComment() - Method in class alun.genio.LinkageLocus

Returns the comment string from the first line of input associated with this locus.

fix(double[][]) - Method in class alun.genepi.AlleleErrorPenetrance

fix(double[][]) - Method in class alun.genepi.AllelePenetrance

fix(double) - Method in class alun.genepi.FixedRecombination

fix(double) - Method in class alun.genepi.OneTheta

fix(int) - Method in class alun.genepi.VariableRecombination

fix(int) - Method in class alun.mcld.Observation

fixedInheritancesProduct() - Method in class alun.genepi.LocusVariables

FixedRecombination - Class in alun.genepi

FixedRecombination(Inheritance, Inheritance, double) - Constructor for class alun.genepi.FixedRecombination

flash(Color) - Method in class alun.mcld.DiploGUI

flash() - Method in class alun.viewgraph.MapCoordinator

flip() - Method in class alun.genepi.Inheritance

flip() - Method in class alun.viewgraph.MapCoordinator

format(int, int) - Static method in class alun.util.StringFormatter

Returns the given int, x, as a String in s character places.

format(int, int, char) - Static method in class alun.util.StringFormatter

format(double, int) - Static method in class alun.util.StringFormatter

Returns a String representation of the given double to s decimal places.

format(double, int, int) - Static method in class alun.util.StringFormatter

format(String, int) - Static method in class alun.util.StringFormatter

formatGuesses(Observation, GeneticDataSource) - Static method in class alun.gchap.HapFormatter

Returns a string representation of the most likely pair of haplotypes for each observed phenotype.

formatHaplotypes(Observation) - Static method in class alun.gchap.HapFormatter

Returns a string representation of the haplotypes and frequencies for the given observation set.

founderGenotypes() - Method in class alun.genepi.LocusVariables

FrameQuitter - Class in alun.view

FrameQuitter() - Constructor for class alun.view.FrameQuitter

freq - Variable in class alun.genio.LinkageLocus

Function - Interface in alun.markov

A Function is a mapping from the states of a set of variables to a double.

G

GCHap - Class in alun.gchap

This class just has a main method in it to run the gene counting program.

GCHap() - Constructor for class alun.gchap.GCHap

GCHap - Class in <Unnamed>

This program finds maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals.

GCHap() - Constructor for class GCHap

geneCount(int) - Method in class alun.gchap.GeneticTrait

Runs n iterations of the gene counting algorithm for the trait.

geneCount(LinkageDataSet) - Static method in class alun.genepi.GeneCounter

geneCount(LinkageDataSet, boolean, double, int, double) - Static method in class alun.genepi.GeneCounter

GeneCountAlleles - Class in <Unnamed>

This program calculates maximum likelihood estimates of allele frequencies from genotypes observed in individuals related in pedigrees.

GeneCountAlleles() - Constructor for class GeneCountAlleles

GeneCounter - Class in alun.genepi

GeneCounter() - Constructor for class alun.genepi.GeneCounter

geneCountToConvergence() - Method in class alun.gchap.Observation

Performs gene counting on this observation until we get some sort of convergence.

GeneticDataSource - Interface in alun.genio

GeneticFunction - Class in alun.genepi

GeneticFunction() - Constructor for class alun.genepi.GeneticFunction

GeneticTrait - Class in alun.gchap

A genetic trait links together a locus with phenotypes.

GeneticTrait(Locus) - Constructor for class alun.gchap.GeneticTrait

Creates a new genetic trait for the given locus.

GeneticVariable - Class in alun.genepi

GeneticVariable(int) - Constructor for class alun.genepi.GeneticVariable

Genotype - Class in alun.gchap

Represents a genotype as an un ordered pair of allele indexes.

Genotype(int, int) - Constructor for class alun.gchap.Genotype

Creates a new genotype from the given allele numbers.

Genotype - Class in alun.genepi

A variable representing the ordered genotype for an individual as some genetic locus.

Genotype(int) - Constructor for class alun.genepi.Genotype

GenotypeModel - Class in alun.genepi

GenotypeModel(Product) - Constructor for class alun.genepi.GenotypeModel

GenotypeModel(Product, Collection<Variable>) - Constructor for class alun.genepi.GenotypeModel

GenotypeModel(Product, Variable) - Constructor for class alun.genepi.GenotypeModel

GenotypePrior - Class in alun.genepi

A function that returns the prior probability of the genotype as the product of the priors for the paternal and maternal alleles.

GenotypePrior(Genotype, double[]) - Constructor for class alun.genepi.GenotypePrior

genotypes() - Method in class alun.genepi.LocusVariables

get(Object) - Method in class alun.graph.MapAsCollection

get(Object, Object) - Method in class alun.util.HashOfHash

Gets the object keyed by the given objects.

get(Object) - Method in class alun.util.HashOfHash

Returns the hashtable keyed by the object a.

get() - Method in class alun.util.HashOfHash

Returns the hashtable in which the other hashtables are keyed.

get(int, int) - Method in class alun.util.Lattice

Gets the Object currently stored at the point (i,j).

get(double, double) - Method in class alun.viewgraph.MapCoordinator

getAllComponent(Mappable) - Method in class alun.viewgraph.DynamicMap

getAllComponent(Mappable) - Method in class alun.viewgraph.DynamicMappableMap

getAllComponent(Mappable) - Method in interface alun.viewgraph.MappableGraph

getAllComponent(Mappable) - Method in class alun.viewgraph.StaticMap

getAllele(int, int) - Method in interface alun.mcld.HaplotypeSource

getAllele(int, int) - Method in class alun.mcld.LDSampler

getAllele() - Method in class alun.mcld.Observation

getAllele(int, int) - Method in class alun.mcld.PerfectHaplotypes

getAllNeighbours(Mappable) - Method in class alun.viewgraph.DynamicMap

getAllNeighbours(Mappable) - Method in class alun.viewgraph.DynamicMappableMap

getAllNeighbours(Mappable) - Method in interface alun.viewgraph.MappableGraph

getAllNeighbours(Mappable) - Method in class alun.viewgraph.StaticMap

getAllVertices() - Method in class alun.viewgraph.DynamicMap

getAllVertices() - Method in class alun.viewgraph.DynamicMappableMap

getAllVertices() - Method in interface alun.viewgraph.MappableGraph

getAllVertices() - Method in class alun.viewgraph.StaticMap

getAnneal() - Method in class alun.mcld.AnnealMover

getAnneal() - Method in class alun.mcld.HaploGUI

getArray() - Method in class alun.markov.DenseTable

getAttributes() - Method in class alun.view.PageType

getBasePairDistance(int, int) - Method in class alun.genio.LinkageInterface

getBestGraph() - Method in class alun.mcld.JointScheme

getBestScore() - Method in class alun.mcld.JointScheme

getBlock() - Method in class alun.genepi.AuxiliaryVariable

getCalculator() - Method in class alun.mcld.JointScheme

getCanvas() - Method in class alun.view.ViewingApplet

getColor() - Method in class alun.viewgraph.AbstractMappable

Gets the colour of the object.

getColor() - Method in class alun.viewgraph.Line

getCoordinator() - Method in class alun.viewgraph.MapViewer

getCount() - Method in class alun.mcld.Locus

getCurrentGraph() - Method in class alun.mcld.JointScheme

getCurrentScore() - Method in class alun.mcld.JointScheme

getData() - Method in class alun.gchap.Observation

getDelta() - Method in class alun.viewgraph.MapViewer

getDone() - Method in class alun.mcld.HaploGUI

getDone() - Method in class alun.mcld.Locus

getDouble() - Method in class alun.util.InputFormatter

Returns the value of the current token as a double.

getEdges() - Method in interface alun.graph.EdgedGraph

getEdges() - Method in class alun.graph.EdgedNetwork

getEdges() - Method in class alun.graph.MaskedNetwork

getError() - Method in class alun.genepi.ErrorPrior

getError(int, int) - Method in class alun.genepi.LociVariables

getFemaleRecomFrac(int, int) - Method in interface alun.genio.GeneticDataSource

Returns the probability of a recombination between loci i and j in a single meiosis in females.

getFemaleRecomFrac(int, int) - Method in class alun.genio.LinkageInterface

getFill() - Method in class alun.viewgraph.Arrow

getFinal() - Method in class alun.markov.GraphicalModel

getFinals() - Method in class alun.markov.GraphicalModel

getFrequency() - Method in class alun.gchap.Phenotype

Returns the number of times the phenotype has been observed.

getFunctions() - Method in class alun.markov.Product

getFunctions(Variable) - Method in class alun.markov.Product

getFunctions(Collection<Variable>) - Method in class alun.markov.Product

getGeneticDistance(int, int) - Method in interface alun.genio.GeneticDataSource

Returns the genetic distance in cM between loci i and j.

getGeneticDistance(int, int) - Method in class alun.genio.LinkageInterface

Returns genetic distance measured in cM between the ith and jth loci.

getGeneticDistance(int, int) - Method in class alun.genio.LinkageParameterData

getGenotype(int, int) - Method in class alun.genepi.LociVariables

getGraph() - Method in class alun.mcld.DecomposableSearch

getGraph() - Method in interface alun.mcld.GraphMHScheme

getGraph() - Method in class alun.mcld.IntervalSearch

getGraphics() - Method in class alun.view.ActiveCanvas

getHaplotype(int) - Method in interface alun.mcld.HaplotypeSource

getHaplotype(int) - Method in class alun.mcld.LDSampler

getHaplotype(int) - Method in class alun.mcld.PerfectHaplotypes

getHaplotypeSource() - Method in class alun.mcld.JointScheme

getHaplotypeSource() - Method in class alun.mcld.LikelihoodCalculator

getHeight() - Method in class alun.view.PageType

getId() - Method in class alun.genepi.Genotype

getIndex() - Method in class alun.mcld.Locus

getIndividuals() - Method in class alun.genio.LinkagePedigreeData

Returns the array of individual data structures.

getInheritance(int, int, int) - Method in class alun.genepi.LociVariables

getInitialBlocks() - Method in class alun.genepi.IndependentLocusSampler

getInt() - Method in class alun.util.InputFormatter

Returns the value of the current token as an int.

getIntervals() - Method in class alun.util.IntervalTree

getInvol() - Method in class alun.mcld.Locus

getInvolTable() - Method in class alun.markov.Clique

getJobAttributes() - Method in class alun.view.PageType

getKids() - Method in class alun.genio.Family

getLDModel(Graph<Locus>) - Method in class alun.mcld.LikelihoodCalculator

getLDModel(Graph<Locus>, boolean) - Method in class alun.mcld.LikelihoodCalculator

getLeft() - Method in class alun.mcld.Locus

getLeft() - Method in interface alun.util.Interval

getLength() - Method in class alun.mcld.Locus

getLength() - Method in interface alun.util.Interval

getLiabilities() - Method in class alun.genio.AffectionStatusLocus

Returns the two dimentional array containing the liability data.

getLocal(E, double) - Method in class alun.util.RadixPlaneSorter

getLocalX(E, double) - Method in class alun.util.RadixPlaneSorter

getLoci() - Method in class alun.genio.LinkageParameterData

Returns the array of loci in this set of data.

getLoci() - Method in interface alun.mcld.HaplotypeSource

getLoci() - Method in class alun.mcld.LDModel

getLoci() - Method in class alun.mcld.LDSampler

getLoci() - Method in class alun.mcld.PerfectHaplotypes

getLocus() - Method in class alun.gchap.GeneticTrait

Returns the asssociated locus.

getLocus() - Method in class alun.genio.LinkagePhenotype

Gets the locus associated with this phenotype.

getLocusBlocks() - Method in class alun.genepi.IndependentLocusSampler

getLocusVariables() - Method in class alun.genepi.LociVariables

getLogValue() - Method in class alun.markov.Product

getMa() - Method in class alun.genio.Family

getMaleRecomFrac(int, int) - Method in interface alun.genio.GeneticDataSource

Returns the probability of a recombination between loci i and j in a single meiosis in males.

getMaleRecomFrac(int, int) - Method in class alun.genio.LinkageInterface

getMap() - Method in class alun.viewgraph.MapViewer

getMarginal(Variable) - Method in class alun.markov.GraphicalModel

getMats() - Method in class alun.genepi.AuxiliaryVariable

getMax() - Method in class alun.markov.GraphicalModel

getMaximizing() - Method in class alun.mcld.DiploGUI

getMiddle() - Method in class alun.mcld.Locus

getMiddle() - Method in interface alun.util.Interval

getMouser() - Method in class alun.view.ViewingApplet

getMover() - Method in class alun.viewgraph.MapViewer

getNeighbours(Object) - Method in class alun.graph.DirectedNetwork

getNeighbours(Object) - Method in class alun.graph.EdgedDirectedNetwork

getNeighbours(Object) - Method in interface alun.graph.Graph

getNeighbours(Object) - Method in class alun.graph.MaskedNetwork

getNeighbours(Object) - Method in class alun.graph.Network

getNeighbours(Object) - Method in class alun.markov.Product

getNeighbours(Object) - Method in class alun.util.IntervalTreeGraph

getNParameters() - Method in class alun.viewgraph.MapMover

getNStates() - Method in class alun.markov.BasicVariable

getNStates() - Method in class alun.markov.CompoundVariable

getNStates() - Method in class alun.markov.MutableSpaceVariable

getNStates() - Method in interface alun.markov.Variable

Returns the number of statest that the Variable can take.

getNStates() - Method in class alun.mcld.Locus

getOutline() - Method in class alun.viewgraph.AbstractMappable

Gets the colour of the outline.

getOutputTable() - Method in class alun.markov.Clique

getPa() - Method in class alun.genio.Family

getPanel() - Method in class alun.view.ScrollWidget

getParameterData() - Method in class alun.genio.LinkageDataSet

Returns the object containting the data from the linkage .par file.

getParameterInit(int) - Method in class alun.mcld.AnnealMover

getParameterInit(int) - Method in class alun.viewgraph.DagMover

getParameterInit(int) - Method in class alun.viewgraph.LocalMover

getParameterInit(int) - Method in class alun.viewgraph.MapMover

getParameterName(int) - Method in class alun.mcld.AnnealMover

getParameterName(int) - Method in class alun.viewgraph.DagMover

getParameterName(int) - Method in class alun.viewgraph.LocalMover

getParameterName(int) - Method in class alun.viewgraph.MapMover

getParameterPenalty() - Method in class alun.mcld.JointScheme

getParameterScale(int) - Method in class alun.mcld.AnnealMover

getParameterScale(int) - Method in class alun.viewgraph.DagMover

getParameterScale(int) - Method in class alun.viewgraph.LocalMover

getParameterScale(int) - Method in class alun.viewgraph.MapMover

getPats() - Method in class alun.genepi.AuxiliaryVariable

getPedigree() - Method in class alun.genio.LinkagePedigreeData

Creates a checked Pedigree structure from the list of individuals.

getPedigreeData() - Method in class alun.genio.LinkageDataSet

Returns the object containing the data from the linkage .ped file.

getPhenotype(int) - Method in class alun.genio.LinkageIndividual

getPhenotypes() - Method in class alun.genio.LinkageIndividual

Returns the array of linkage phonetypes for this individual.

getPhysicalDistance(int, int) - Method in interface alun.genio.GeneticDataSource

Returns the physical distance in Mb between loci i and j.

getPhysicalDistance(int, int) - Method in class alun.genio.LinkageInterface

Returns the physical distance between the ith and jth loci calculated from the genetic distance at the rate of 1cM = 1Mb.

getPhysicalDistance(int, int) - Method in class alun.genio.LinkageParameterData

getPosition() - Method in class alun.mcld.Locus

getProduct() - Method in class alun.mcld.LDSampler

getRealValue() - Method in class alun.view.ScrollWidget

getRight() - Method in class alun.mcld.Locus

getRight() - Method in interface alun.util.Interval

getSearchScheme() - Method in class alun.mcld.JointScheme

getShowing(double, double) - Method in class alun.viewgraph.DynamicMap

getShowing(double, double) - Method in class alun.viewgraph.DynamicMappableMap

getShowing(double, double) - Method in interface alun.viewgraph.MappableGraph

getShowing(double, double) - Method in class alun.viewgraph.StaticMap

getShownComponent(Mappable) - Method in class alun.viewgraph.DynamicMap

getShownComponent(Mappable) - Method in class alun.viewgraph.DynamicMappableMap

getShownComponent(Mappable) - Method in interface alun.viewgraph.MappableGraph

getShownComponent(Mappable) - Method in class alun.viewgraph.StaticMap

getShownInNeighbours(Mappable) - Method in class alun.viewgraph.DynamicMap

getShownInNeighbours(Mappable) - Method in class alun.viewgraph.DynamicMappableMap

getShownInNeighbours(Mappable) - Method in interface alun.viewgraph.MappableGraph

getShownInNeighbours(Mappable) - Method in class alun.viewgraph.StaticMap

getShownNeighbours(Mappable) - Method in class alun.viewgraph.DynamicMap

getShownNeighbours(Mappable) - Method in class alun.viewgraph.DynamicMappableMap

getShownNeighbours(Mappable) - Method in interface alun.viewgraph.MappableGraph

getShownNeighbours(Mappable) - Method in class alun.viewgraph.StaticMap

getShownOutNeighbours(Mappable) - Method in class alun.viewgraph.DynamicMap

getShownOutNeighbours(Mappable) - Method in class alun.viewgraph.DynamicMappableMap

getShownOutNeighbours(Mappable) - Method in interface alun.viewgraph.MappableGraph

getShownOutNeighbours(Mappable) - Method in class alun.viewgraph.StaticMap

getShownVertices() - Method in class alun.viewgraph.DynamicMap

getShownVertices() - Method in class alun.viewgraph.DynamicMappableMap

getShownVertices() - Method in interface alun.viewgraph.MappableGraph

getShownVertices() - Method in class alun.viewgraph.StaticMap

getState() - Method in class alun.markov.BasicVariable

getState() - Method in class alun.markov.CompoundVariable

getState() - Method in class alun.markov.MutableSpaceVariable

getState() - Method in interface alun.markov.Variable

Returns the value of the current state of the Variable.

getState() - Method in class alun.mcld.Locus

getStateIndex() - Method in class alun.markov.BasicVariable

getStateIndex() - Method in class alun.markov.CompoundVariable

getStateIndex() - Method in class alun.markov.MutableSpaceVariable

getStateIndex() - Method in interface alun.markov.Variable

Returns the index of the current state of the Variable.

getStateIndex() - Method in class alun.mcld.Locus

getString() - Method in class alun.util.InputFormatter

Returns the value of the current token as a String.

getTheta(int, int) - Method in class alun.genio.LinkageInterface

Returns the recombination fraction between the ith and jth loci calculated as the Kosambi function of the genetic distance.

getTheta(int, int) - Method in class alun.genio.LinkageParameterData

getThread() - Method in class alun.view.ViewingApplet

getTrait() - Method in class alun.gchap.Observation

Returns the trait for which this is an observation.

getTriplet(Object) - Method in class alun.genio.Pedigree

getTripletClique(Set<Variable>, Product) - Method in class alun.genepi.GenotypeModel

getValue() - Method in class alun.genepi.AlleleErrorPenetrance

getValue() - Method in class alun.genepi.AllelePenetrance

getValue() - Method in class alun.genepi.AllelePrior

getValue() - Method in class alun.genepi.AuxLinkFunction

getValue() - Method in class alun.genepi.AuxLocusFunction

getValue() - Method in class alun.genepi.ErrorPenetrance

getValue() - Method in class alun.genepi.ErrorPrior

&nb