Spec
HmmGraphA grap representing a Hidden Markov Model (HMM).
A grap representing a Hidden Markov Model (HMM).
Extends | Graph |
---|---|
All Extended | Graph |
All Impl'd | AssignableConcept, ContainerConcept, DestructibleConcept |
Defined in | <seqan/graph_types.h> |
Signature |
template <[typename TAlphabet[, typename TCargo[, typename TSpec]]]>
class Graph<Hmm<TAlphabet, TCargo, TSpec> >;
|
Template Parameters
TAlphabet |
The alphabet of the HMM. Default: Dna. |
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TCargo |
The edge cargos. Default: void. |
TSpec |
The specialization type. Default: Default. Use WithoutEdgeIds here to omit edge ids. NB: if edges do not store ids then external property maps do not work. |
Interface Function Overview
-
void assignBeginState(hmm, v);
Assigns a begin state. -
void assignEmissionProbability(hmm, state, symbol, eProb);
Assigns a new emission probability. -
void assignEndState(hmm, v);
Assigns a end state. -
void assignSilentStatus(hmm, v, silent);
Assigns a silent status to a state. -
void assignTransitionProbability(hmm, state1, state2, prob);, void assignTransitionProbability(hmm, e, prob);
Assigns a new transition probability to an existing edge. -
TVertexDescriptor beginState(hmm);
Return a reference to the begin state vertex descriptor. -
TCargo emissionProbability(hmm, state, symbol);
Returns a reference to the emissions probability. -
TVertexDescriptor endState(hmm);
Return a reference to the end state vertex descriptor. -
TVertexDescriptor getBeginState(hmm);
Return the begin state vertex descriptor. -
TCargo getEmissionProbability(hmm, state, symbol);
Returns the emissions probability. -
TVertexDescriptor getEndState(hmm);
Return the end state vertex descriptor. -
TCargo getTransitionProbability(hmm, state1, state2);, TCargo getTransitionProbability(hmm, e);
Returns the transition probability, stored as the cargo. -
bool isSilent(hmm, v);
Indicates whether a state is silent or not. -
TBoolRef silentStatus(hmm, v);
Return reference to silent status flag. -
TCargo getTransitionProbability(hmm, state1, state2);, TCargo getTransitionProbability(hmm, e);
Returns a reference to transition probability, stored as the cargo.
Interface Functions Inherited From Graph
addEdge
addEdges
addVertex
assignEdgeMap
assignVertexMap
clear
clearEdges
clearVertices
degree
empty
findEdge
getAdjacencyMatrix
getNil
getVertexAdjacencyVector
inDegree
numEdges
numVertices
outDegree
removeEdge
removeInEdges
removeOutEdges
removeVertex
resizeEdgeMap
resizeVertexMap
sourceVertex
targetVertex
transpose
writeRecords
Interface Functions Inherited From AssignableConcept
Interface Functions Inherited From ContainerConcept
Interface Metafunction Overview
Interface Metafunctions Inherited From Graph
Interface Metafunctions Inherited From ContainerConcept
Detailed Description
An HMM is a directed graph with edges labeled with transition probabilities and emission profiles for each vertex. Vertices correspond to states in an HMM.
Interface Functions Detail
void assignBeginState(hmm, v);
Assigns a begin state.
Parameters
hmm
|
The HmmGraph to assign the begin state of. |
---|---|
v
|
The descriptor of the vertex to assign as begin state. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
void assignEmissionProbability(hmm, state, symbol, eProb);
Assigns a new emission probability.
Parameters
hmm
|
The HmmGraph to query. |
---|---|
state
|
A vertex descriptor with the source state. |
symbol
|
The symbol. Type: TAlphabet. |
eProb
|
Emission probability to assign. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
void assignEndState(hmm, v);
Assigns a end state.
Parameters
hmm
|
The HmmGraph to assign the end state of. |
---|---|
v
|
The descriptor of the vertex to assign as end state. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
void assignSilentStatus(hmm, v, silent);
Assigns a silent status to a state.
Parameters
hmm
|
The HmmGraph to assign the silent status in. |
---|---|
v
|
Vertex descriptor of the state to assign silent status. |
silent
|
A bool with the silent status. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
void assignTransitionProbability(hmm, state1, state2, prob);
void assignTransitionProbability(hmm, e, prob);
Assigns a new transition probability to an existing edge.
Parameters
hmm
|
The HmmGraph to get transition probability for. |
---|---|
state1
|
Assign transition probability from start state1. |
state2
|
Assign probability to target state2. |
e
|
Assign probability to edge with this edge descriptor. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TVertexDescriptor beginState(hmm);
Return a reference to the begin state vertex descriptor.
Parameters
hmm
|
The HmmGraph to get the vertex descriptor of. |
---|
Returns
TVertexDescriptor |
A reference to the begin state vertex descriptor. |
---|
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TCargo emissionProbability(hmm, state, symbol);
Returns a reference to the emissions probability.
Parameters
hmm
|
The HmmGraph to query. |
---|---|
state
|
A vertex descriptor with the source state. |
symbol
|
The symbol. Type: TAlphabet. |
Returns
TCargo |
Reference to the emission probability. |
---|
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TVertexDescriptor endState(hmm);
Return a reference to the end state vertex descriptor.
Parameters
hmm
|
The HmmGraph to get the vertex descriptor of. |
---|
Returns
TVertexDescriptor |
A reference to the end state vertex descriptor. |
---|
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TVertexDescriptor getBeginState(hmm);
Return the begin state vertex descriptor.
Parameters
hmm
|
The HmmGraph to get the vertex descriptor of. |
---|
Returns
TVertexDescriptor |
The begin state vertex descriptor. |
---|
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TCargo getEmissionProbability(hmm, state, symbol);
Returns the emissions probability.
Parameters
hmm
|
The HmmGraph to query. |
---|---|
state
|
A vertex descriptor with the source state. |
symbol
|
The symbol. Type: TAlphabet. |
Returns
TCargo |
The emission probability. |
---|
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TVertexDescriptor getEndState(hmm);
Return the end state vertex descriptor.
Parameters
hmm
|
The HmmGraph to get the vertex descriptor of. |
---|
Returns
TVertexDescriptor |
The end state vertex descriptor. |
---|
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TCargo getTransitionProbability(hmm, state1, state2);
TCargo getTransitionProbability(hmm, e);
Returns the transition probability, stored as the cargo.
Parameters
hmm
|
The HmmGraph to get transition probability for. |
---|---|
state1
|
Return transition probability from start state1. |
state2
|
Return transition probability to target state2. |
e
|
An edge descriptor. |
Returns
TCargo |
Return the transition probability. |
---|
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
bool isSilent(hmm, v);
Indicates whether a state is silent or not.
Parameters
hmm
|
The HmmGraph to query. |
---|---|
v
|
Vertex descriptor of the state to query. |
Returns
bool |
true if the state is silent and false if not. |
---|
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TBoolRef silentStatus(hmm, v);
Return reference to silent status flag.
Parameters
hmm
|
The HmmGraph to assign the silent status in. |
---|---|
v
|
Vertex descriptor of the state to assign silent status. |
Returns
TBoolRef |
Reference to bool silent status flag. |
---|
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TCargo getTransitionProbability(hmm, state1, state2);
TCargo getTransitionProbability(hmm, e);
Returns a reference to transition probability, stored as the cargo.
Parameters
hmm
|
The HmmGraph to get transition probability for. |
---|---|
state1
|
Return transition probability from start state1. |
state2
|
Return transition probability to target state2. |
e
|
An edge descriptor. |
Returns
TCargo |
Returns a reference to the transition probability. |
---|
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.