org.agmodel.bioinfo.segregation
Class TwoPointAnalysis

java.lang.Object
  extended byorg.agmodel.bioinfo.segregation.TwoPointAnalysis

public class TwoPointAnalysis
extends java.lang.Object


Constructor Summary
TwoPointAnalysis()
           
 
Method Summary
 double getR_BC(char[] l1, char[] l2)
           
 double getR_DH(char[] l1, char[] l2)
           
 double getR_F2(char[] l1, char[] l2, int markerType1, int markerType2)
           
 double getR_RIL(char[] l1, char[] l2)
           
 RecombinationBean getRecombinationBean_BC(char[] l1, char[] l2)
          Calculate recombination rate for backcross
 RecombinationBean getRecombinationBean_DH(char[] l1, char[] l2)
          Calculate recombination rate for doubled haploid
 RecombinationBean getRecombinationBean_F2(char[] l1, char[] l2, int markerType1, int markerType2)
          Calculate recombination rate for F2
 RecombinationBean getRecombinationBean_RIL(char[] l1, char[] l2)
          Calculate recombination rate for recombinant inbred line
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

TwoPointAnalysis

public TwoPointAnalysis()
Method Detail

getR_BC

public double getR_BC(char[] l1,
                      char[] l2)

getR_DH

public double getR_DH(char[] l1,
                      char[] l2)

getR_RIL

public double getR_RIL(char[] l1,
                       char[] l2)

getR_F2

public double getR_F2(char[] l1,
                      char[] l2,
                      int markerType1,
                      int markerType2)

getRecombinationBean_BC

public RecombinationBean getRecombinationBean_BC(char[] l1,
                                                 char[] l2)
Calculate recombination rate for backcross

Parameters:
l1 - Array of genotypes for locus1 ('A' (homozygote for the recurrent parent genotype), 'H' (heterozogote), '-' (missing data))
l2 - Array of genotypes for locus2 (Genotype description is the same as locus1)
Returns:
RecombinationBean.

getRecombinationBean_DH

public RecombinationBean getRecombinationBean_DH(char[] l1,
                                                 char[] l2)
Calculate recombination rate for doubled haploid

Parameters:
l1 - Array of genotypes for locus1 ('A' (homozygote for parental genotype a), 'B' (homozygote for paretnal genotype b), '-' (missing data))
l2 - Array of gneotypes for locus2 (Genotype description is the same as locus1)
Returns:
Recombination rate (If array size of l1 and l2 is not identical, return -1).

getRecombinationBean_RIL

public RecombinationBean getRecombinationBean_RIL(char[] l1,
                                                  char[] l2)
Calculate recombination rate for recombinant inbred line

Parameters:
l1 - Array of genotypes for locus1 ('A' (homozygote for parental genotype a), 'B' (homozygote for paretnal genotype b), '-' (missing data))
l2 - Array of gneotypes for locus2 (Genotype description is the same as locus1)
Returns:
Recombination rate (If array size of l1 and l2 is not identical, return -1).

getRecombinationBean_F2

public RecombinationBean getRecombinationBean_F2(char[] l1,
                                                 char[] l2,
                                                 int markerType1,
                                                 int markerType2)
Calculate recombination rate for F2

Parameters:
l1 - Array of genotypes for locus1 ('A' (homozygote for parental genotype a), 'B' (homozygote for paretnal genotype b), 'H' (heterozygote carrying both alleles a and b), 'C' (not a homozygote for allele a (either bb or ab genotype)), 'D' (not a homozygote for allele b (either aa or ab genotype)), '-' (missing data))
l2 - Array of gneotypes for locus2 (Genotype description is the same as locus1)
Returns:
Recombination rate (If array size of l1 and l2 is not identical, return -1).