Package vcf

Class PositionMap

java.lang.Object

vcf.PositionMap

All Implemented Interfaces:

GeneticMap

public class PositionMap
extends java.lang.Object
implements GeneticMap

Class PositionMap represents a genetic map obtained by multiplying chromosome position by a scale factor.

Instances of class PositionMap are immutable.

Constructor Summary

Constructors

Constructor	Description
PositionMap(double scaleFactor)	Constructs a new PositionMap instance.

Method Summary

Modifier and Type	Method	Description
int	basePos(int chrom, double geneticPosition)	Returns the base position corresponding to the specified genetic map position.
double	genPos(int chrom, int basePosition)	Returns the genetic map position of the specified genome coordinate.
double	genPos(Marker marker)	Returns the genetic map position of the specified marker.
double	scaleFactor()	Returns the scale factor that is multiplied by the chromosome position to obtain the corresponding genetic map position

Methods inherited from interface vcf.GeneticMap

genPos, pRecomb, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PositionMap

public PositionMap(double scaleFactor)

Constructs a new PositionMap instance.

Parameters:

scaleFactor - the factor that is multiplied by a base position to obtain the corresponding genetic map position

Throws:

java.lang.IllegalArgumentException - if scaleFactor <= 0d || Double.isFinite(scaleFactor) == false

Method Detail

scaleFactor

public double scaleFactor()

Returns the scale factor that is multiplied by the chromosome position to obtain the corresponding genetic map position

Returns:

the scale factor.

basePos

public int basePos(int chrom,
                   double geneticPosition)

Description copied from interface: GeneticMap

Returns the base position corresponding to the specified genetic map position. If the genetic position is not a map position then the base position is estimated from the nearest genetic map positions using linear interpolation.

Specified by:

basePos in interface GeneticMap

Parameters:

chrom - the chromosome index

geneticPosition - the genetic position on the chromosome

Returns:

the base position corresponding to the specified genetic map position

genPos

public double genPos(Marker marker)

Description copied from interface: GeneticMap

Returns the genetic map position of the specified marker. The genetic map position is estimated using linear interpolation.

Specified by:

genPos in interface GeneticMap

Parameters:

marker - a genetic marker

Returns:

the genetic map position of the specified marker

genPos

public double genPos(int chrom,
                     int basePosition)

Description copied from interface: GeneticMap

Returns the genetic map position of the specified genome coordinate. The genetic map position is estimated using linear interpolation.

Specified by:

genPos in interface GeneticMap

Parameters:

chrom - the chromosome index

basePosition - the base coordinate on the chromosome

Returns:

the genetic map position of the specified genome coordinate