public final class ImpStates
extends java.lang.Object
Class ImpStates
identifies a list of pseudo-reference haplotypes
for a target haplotype. Each pseudo-reference haplotype is a
one-dimensional mosaic of reference haplotype segments.
Instances of ImpStates
are not thread-safe.
Constructor | Description |
---|---|
ImpStates(ImpIbs ibsHaps) |
Constructs a new
ImpStates object from the specified data. |
Modifier and Type | Method | Description |
---|---|---|
int |
ibsStates(int targHap,
int[][] hapIndices,
boolean[][] alMatch) |
Stores the reference haplotype for the
j -th state
at the m -th marker in hapIndices[m][j] , and stores
the equality of the allele carried by the reference haplotype for
the j -th state and the allele carried by the target haplotype
at the m -th marker in alMatch[m][j] . |
int |
nStates() |
Returns the number of HMM states per marker.
|
public ImpStates(ImpIbs ibsHaps)
ImpStates
object from the specified data.ibsHaps
- the IBS haplotype segmentsjava.lang.NullPointerException
- if
impData == null || ibsStates == null
public int nStates()
public int ibsStates(int targHap, int[][] hapIndices, boolean[][] alMatch)
j
-th state
at the m
-th marker in hapIndices[m][j]
, and stores
the equality of the allele carried by the reference haplotype for
the j
-th state and the allele carried by the target haplotype
at the m
-th marker in alMatch[m][j]
. The number of
HMM states states at each marker is returned.targHap
- the haplotype indexhapIndices
- the two-dimensional array in which
reference haplotype indices for each HMM state will be storedalMatch
- the two-dimensional array in which allele match status
between the target haplotype and HMM state will be storedjava.lang.IndexOutOfBoundsException
- if
targHap < 0 || targHap >= this.nTargHaps()
java.lang.IndexOutOfBoundsException
- if
(hapIndices.length < this.impData().nClusters())
or if any
hapIndices[j].length
is less than the number of HMM states
at a marker for any j
satisfying
(0 <= j && j < this.nClusters())
java.lang.IndexOutOfBoundsException
- if
(alMatch.length < this.impdata().nClusters())
or if any
alMatch[j].length
is less than the number of HMM states
at a marker for any j
satisfying
(0 <= j && j < this.nClusters())
java.lang.NullPointerException
- if
(hapIndices == null)
or if (hapIndices[j] == null)
for
any j
satisfying (0 <= j && j < this.nClusters())
java.lang.NullPointerException
- if
(alMatch == null)
or if (alMatch[j] == null)
for
any j
satisfying (0 <= j && j < this.nClusters())