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.
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.
|
genPos, pRecomb, toString
public static MarkerMap create(GeneticMap genMap, Markers markers)
MarkerMap
instance that is constructed from the
specified datagenMap
- the genetic mapmarkers
- a list of markersMarkerMap
instancejava.lang.IllegalArgumentException
- if
markers.marker(0).chromIndex()
!= markers.marker(markers.nMarkers()-1).chromIndex()
java.lang.NullPointerException
- if genMap == null || markers == null
public java.lang.String chrom()
public int chromIndex()
public int basePos(int chrom, double geneticPosition)
GeneticMap
basePos
in interface GeneticMap
chrom
- the chromosome indexgeneticPosition
- the genetic position on the chromosomepublic double genPos(Marker marker)
GeneticMap
genPos
in interface GeneticMap
marker
- a genetic markerpublic double genPos(int chrom, int basePosition)
GeneticMap
genPos
in interface GeneticMap
chrom
- the chromosome indexbasePosition
- the base coordinate on the chromosomepublic int nMarkers()
public Markers markers()
public Marker marker(int marker)
marker
- a marker indexpublic double genPos(int marker)
marker
- a marker indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
public double[] genPos()
k
-th element
equals this.genPos(k)
.