Package vcf

Class MarkerMap

java.lang.Object

vcf.MarkerMap

All Implemented Interfaces:

GeneticMap

public class MarkerMap
extends java.lang.Object
implements GeneticMap

Class MarkerMap represents genetic map positions for a list of markers.

Instances of class MarkerMap are immutable.

Method Summary

Modifier and Type	Method	Description
int	basePos(int chrom, double geneticPosition)	Returns the base position corresponding to the specified genetic map position.
java.lang.String	chrom()	Returns the chromosome corresponding to the list of markers.
int	chromIndex()	Returns the index of the chromosome corresponding to the list of markers.
static MarkerMap	create(GeneticMap genMap, Markers markers)	Returns a new MarkerMap instance that is constructed from the specified data
double[]	genPos()	Returns the array of genetic map positions whose k-th element equals this.genPos(k).
double	genPos(int marker)	Returns the genetic map position of the specified marker.
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.
Marker	marker(int marker)	Returns the specified marker.
Markers	markers()	Returns the list of markers.
int	nMarkers()	Returns the number of markers.
MarkerMap	reverse()	Returns a MarkerMap instance that is obtained by reversing the order of markers in this.

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

Method Detail

create

public static MarkerMap create(GeneticMap genMap,
                               Markers markers)

Returns a new MarkerMap instance that is constructed from the specified data

Parameters:

genMap - the genetic map

markers - a list of markers

Returns:

a returns new MarkerMap instance

Throws:

java.lang.IllegalArgumentException - if markers.marker(0).chromIndex() != markers.marker(markers.nMarkers()-1).chromIndex()

java.lang.NullPointerException - if genMap == null || markers == null

reverse

public MarkerMap reverse()

Returns a MarkerMap instance that is obtained by reversing the order of markers in this.

Returns:

a MarkerMap instance that is obtained by reversing the order of markers in this

chrom

public java.lang.String chrom()

Returns the chromosome corresponding to the list of markers.

Returns:

the chromosome corresponding to the list of markers

chromIndex

public int chromIndex()

Returns the index of the chromosome corresponding to the list of markers.

Returns:

the index of the chromosome corresponding to the list of markers

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

nMarkers

public int nMarkers()

Returns the number of markers.

Returns:

the number of markers

markers

public Markers markers()

Returns the list of markers.

Returns:

the list of markers

marker

public Marker marker(int marker)

Returns the specified marker.

Parameters:

marker - a marker index

Returns:

the specified marker

genPos

public double genPos(int marker)

Returns the genetic map position of the specified marker.

Parameters:

marker - a marker index

Returns:

the genetic map position of the specified marker

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

genPos

public double[] genPos()

Returns the array of genetic map positions whose k-th element equals this.genPos(k).

Returns:

the array of genetic map positions