org.agmodel.bioinfo.segregation
Class MapFunction

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

public class MapFunction
extends java.lang.Object


Field Summary
static double MAX_DIST
           
static int MF_HALDANE
           
static java.lang.String MF_HALDANE_NAME
           
static int MF_KOSAMBI
           
static java.lang.String MF_KOSAMBI_NAME
           
 
Constructor Summary
MapFunction()
           
MapFunction(int function)
           
 
Method Summary
 double getDistance(double r)
           
 int getFunction()
           
static java.lang.String getFunctionName(int function)
           
 double getHaldaneDistance(double r)
          Calculate map distance from recombination rate on the basis of Holdane's function
 double getHaldaneRate(double x)
          Calculate recombination rate from map distance on the basis of Holdane's function
 double getKosambiDistance(double r)
          Calculate map distance from recombination rate on the basis of Kosambi's function
 double getKosambiRate(double x)
          Calculate recombination rate from map distance on the basis of Kosambi's function
 double getRate(double x)
           
 void setFunction(int i)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

MF_HALDANE

public static final int MF_HALDANE
See Also:
Constant Field Values

MF_KOSAMBI

public static final int MF_KOSAMBI
See Also:
Constant Field Values

MAX_DIST

public static final double MAX_DIST
See Also:
Constant Field Values

MF_HALDANE_NAME

public static final java.lang.String MF_HALDANE_NAME
See Also:
Constant Field Values

MF_KOSAMBI_NAME

public static final java.lang.String MF_KOSAMBI_NAME
See Also:
Constant Field Values
Constructor Detail

MapFunction

public MapFunction()

MapFunction

public MapFunction(int function)
Method Detail

getRate

public double getRate(double x)

getFunctionName

public static java.lang.String getFunctionName(int function)

getDistance

public double getDistance(double r)

getHaldaneRate

public double getHaldaneRate(double x)
Calculate recombination rate from map distance on the basis of Holdane's function

Parameters:
x - Map distance. The unit is Morgan.
Returns:
Recombination rate.

getHaldaneDistance

public double getHaldaneDistance(double r)
Calculate map distance from recombination rate on the basis of Holdane's function

Parameters:
r - Recombination rate.
Returns:
Map distance. The unit is Morgan.

getKosambiRate

public double getKosambiRate(double x)
Calculate recombination rate from map distance on the basis of Kosambi's function

Parameters:
x - Map distance. The unit is Morgan.
Returns:
Recombination rate.

getKosambiDistance

public double getKosambiDistance(double r)
Calculate map distance from recombination rate on the basis of Kosambi's function

Parameters:
r - Recombinatino rate.
Returns:
Map distance. The unit is Morgan.

getFunction

public int getFunction()
Returns:

setFunction

public void setFunction(int i)
Parameters:
i -