public class SamplerData
extends java.lang.Object
Class SamplerData
contains immutable input data for the
current marker window.
Instances of class SamplerData
are immutable.
Constructor and Description |
---|
SamplerData(Par par,
CurrentData cd,
java.util.List<HapPair> hapPairs,
boolean revMarkers,
RunStats runStats)
Constructs a new
SamplerData instance from the specified data. |
Modifier and Type | Method and Description |
---|---|
float |
err()
Returns the allele error rate
|
GL |
gl()
Returns the genotype likelihoods for the
target samples at the target data markers.
|
Markers |
markers()
returns the list of markers.
|
boolean |
markersAreReversed()
Returns
true if the order of markers is reversed, and
false otherwise |
int |
nHaps()
Returns the number of haplotypes.
|
int |
nMarkers()
Returns the number of markers.
|
int |
nSamples()
Returns the number of samples.
|
Par |
par()
Returns the analysis parameters.
|
float |
pRecomb(int marker)
Returns the probability of recombination between
(marker - 1)
and marker . |
RestrictedDag |
rdag()
Returns the DAG model.
|
public SamplerData(Par par, CurrentData cd, java.util.List<HapPair> hapPairs, boolean revMarkers, RunStats runStats)
SamplerData
instance from the specified data.
The contract for this method is undefined if the specified
hapPairs
is inconsistent with the input data
contained in the cd
parameter.par
- the analysis parameterscd
- the input data for the current marker windowhapPairs
- the target haplotype pairs used to build the haplotype
frequency modelrevMarkers
- true
if the order of markers should
be reversed when building the haplotype frequency model, and
false
otherwiserunStats
- the object to which run-time statistics will be writtenjava.lang.IllegalArgumentException
- if haps.isEmpty() == true
java.lang.NullPointerException
- if any parameter is null
public boolean markersAreReversed()
true
if the order of markers is reversed, and
false
otherwisetrue
if the order of markers is reversed, and
false
otherwisepublic int nMarkers()
public int nSamples()
public int nHaps()
public Markers markers()
public Par par()
public RestrictedDag rdag()
public GL gl()
public float err()
public float pRecomb(int marker)
(marker - 1)
and marker
.marker
- a marker index(marker - 1)
and marker
java.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()