alun.genio
Interface GeneticDataSource

All Superinterfaces:

BasicGeneticData, ParameterData, PedigreeData

All Known Implementing Classes:

LinkageInterface

public interface GeneticDataSource
extends BasicGeneticData

Method Summary

java.lang.String	call(int i, int j) Returns a string representation of the observation for the ith individuals at the jth locus.
java.lang.String	id(int i) Returns a String identifyer for the ith person in the list.
int	indAllele(int i, int j, int k) If k = 0, returns the first allele for the ith individual at the jth locus.
java.lang.String	locName(int j) Returns a String identifier for the jth locus.
java.lang.String	name() The identifier of this data source.
int	nPhenotypes(int j) The number of phenotypes at the jth genetic locus.
int	nProbands() Returns the number of individuals whose proband status > 0.
int	proband(int i) Returns the proband status of the ith individual in the list.

Methods inherited from interface alun.genio.BasicGeneticData

penetrance

Methods inherited from interface alun.genio.ParameterData

alleleFreqs, getFemaleRecomFrac, getMaleRecomFrac, nAlleles, nLoci

Methods inherited from interface alun.genio.PedigreeData

kids, ma, nIndividuals, nuclearFamilies, pa

Method Detail

name

java.lang.String name()

The identifier of this data source.

locName

java.lang.String locName(int j)

Returns a String identifier for the jth locus.

call

java.lang.String call(int i,
                      int j)

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

nPhenotypes

int nPhenotypes(int j)

The number of phenotypes at the jth genetic locus. Must be greater than zero and may be infinite. Phenotype is used to mean any observation for the locus, including genotype information. So for a co-dominant genetic marker nPhenotypes(j) should return the same as nAlleles(j)*(nAlleles(j)-1)/2.

id

java.lang.String id(int i)

Returns a String identifyer for the ith person in the list.

Specified by:

id in interface BasicGeneticData

proband

int proband(int i)

Returns the proband status of the ith individual in the list.

nProbands

int nProbands()

Returns the number of individuals whose proband status > 0.

indAllele

int indAllele(int i,
              int j,
              int k)

If k = 0, returns the first allele for the ith individual at the jth locus. If k = 1, returns the second allele for the ith individual at the jth locus. Allele numbers should start at 0. If such a clear allele call is not possible return -1.