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. |
|---|---|
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
addEdgeaddEdgesaddVertexassignEdgeMapassignVertexMapclearclearEdgesclearVerticesdegreeemptyfindEdgegetAdjacencyMatrixgetNilinDegreenumEdgesnumVerticesoutDegreeremoveEdgeremoveInEdgesremoveOutEdgesremoveVertexresizeEdgeMapresizeVertexMapsourceVertextargetVertextransposewrite
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!