public interface StateProbs
Class StateProbs
stores a subset of Li and Stephens HMM states
and associated probabilities for a target haplotype.
All instances of interface StateProbs
are required to be
immutable.
Modifier and Type | Method | Description |
---|---|---|
int |
nStates(int targMarker) |
Returns the number of stored HMM states at the specified
target marker.
|
int |
nTargMarkers() |
Returns the number of target markers.
|
float |
probs(int targMarker,
int index) |
Returns the probability of the specified state at the specified target
marker.
|
float |
probsP1(int targMarker,
int index) |
Returns the probability of the specified state at the marker following
the specified target marker.
|
int |
refHap(int targMarker,
int index) |
Returns the specified reference haplotype index.
|
int |
targHap() |
Returns the target haplotype index.
|
int targHap()
int nTargMarkers()
int nStates(int targMarker)
targMarker
- a target marker indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nTargMarkers()
int refHap(int targMarker, int index)
targMarker
- a target marker indexindex
- a stored state index at the specified target markerjava.lang.IndexOutOfBoundsException
- if
targMarker < 0 || targMarker >= this.nTargMarkers()
java.lang.IndexOutOfBoundsException
- if
index < 0 || index >= this.nStates(targMarker)
float probs(int targMarker, int index)
targMarker
- a target marker indexindex
- a stored state indexjava.lang.IndexOutOfBoundsException
- if
targMarker < 0 || targMarker >= this.nTargMarkers()
java.lang.IndexOutOfBoundsException
- if
index < 0 || index >= this.nStates(targMarker)
float probsP1(int targMarker, int index)
(targMarker + 1 == this.nTargMarkers())
, the probability of
the specified state at the specified target marker is returned.targMarker
- a target marker indexindex
- a stored state indexjava.lang.IndexOutOfBoundsException
- if
targMarker < 0 || targMarker >= this.nTargMarkers()
java.lang.IndexOutOfBoundsException
- if
index < 0 || index >= this.nStates(targMarker)