Interface for simulations. More...
#include <Bpp/Phyl/Simulation/MutationProcess.h>
Inheritance diagram for bpp::MutationProcess:
Public Member Functions | |
| MutationProcess () | |
| virtual | ~MutationProcess () |
| virtual size_t | mutate (size_t state) const =0 |
| Mutate a character in state i. More... | |
| virtual size_t | mutate (size_t state, unsigned int n) const =0 |
| Mutate a character in state i n times. More... | |
| virtual double | getTimeBeforeNextMutationEvent (size_t state) const =0 |
| Get the time before next mutation event. More... | |
| virtual size_t | evolve (size_t initialState, double time) const =0 |
| Simulation a character evolution during a specified time according to the given substitution model and send the final state. More... | |
| virtual MutationPath | detailedEvolve (size_t initialState, double time) const =0 |
| Simulation a character evolution during a specified time according to the given substitution model and send the total path with all intermediate states and times between mutation events. More... | |
| virtual MutationPath | detailedEvolve (size_t initialState, size_t finalState, double time) const =0 |
| Simulation a character evolution during a specified time according to the given substitution model and send the total path with all intermediate states and times between mutation events, conditional to the final state.q. More... | |
| virtual std::shared_ptr< const SubstitutionModelInterface > | getSubstitutionModel () const =0 |
| Get the substitution model associated to the mutation process. More... | |
Detailed Description
Interface for simulations.
A mutation process defines the rules for mutations to occur. The MutationProcess interface provides two methods, one for mutating a character in state i in another character, another for achieving this task n times.
Definition at line 190 of file MutationProcess.h.
Constructor & Destructor Documentation
◆ MutationProcess()
|
inline |
Definition at line 193 of file MutationProcess.h.
◆ ~MutationProcess()
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inlinevirtual |
Definition at line 194 of file MutationProcess.h.
Member Function Documentation
◆ detailedEvolve() [1/2]
|
pure virtual |
Simulation a character evolution during a specified time according to the given substitution model and send the total path with all intermediate states and times between mutation events.
- Parameters
-
initialState The state before beginning evolution. time The time during which evolution must occur.
- Returns
- The resulting mutation path.
Implemented in bpp::AbstractMutationProcess.
◆ detailedEvolve() [2/2]
|
pure virtual |
Simulation a character evolution during a specified time according to the given substitution model and send the total path with all intermediate states and times between mutation events, conditional to the final state.q.
- Parameters
-
initialState The state before beginning evolution. finalState The state after evolution. time The time during which evolution must occur.
- Returns
- The resulting mutation path.
Implemented in bpp::AbstractMutationProcess.
◆ evolve()
|
pure virtual |
Simulation a character evolution during a specified time according to the given substitution model and send the final state.
- Parameters
-
initialState The state before beginning evolution. time The time during which evolution must occur.
- Returns
- The resulting state after evolution is completed.
Implemented in bpp::SimpleMutationProcess, and bpp::AbstractMutationProcess.
◆ getSubstitutionModel()
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pure virtual |
Get the substitution model associated to the mutation process.
- Returns
- The SubstitutionModel associated to this instance.
Implemented in bpp::AbstractMutationProcess.
◆ getTimeBeforeNextMutationEvent()
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pure virtual |
Get the time before next mutation event.
- Parameters
-
state The actual state of the chain;
- Returns
- A random time before next mutation event.
Implemented in bpp::AbstractMutationProcess.
◆ mutate() [1/2]
|
pure virtual |
Mutate a character in state i.
- Parameters
-
state The current state of the character.
Implemented in bpp::AbstractMutationProcess.
◆ mutate() [2/2]
|
pure virtual |
Mutate a character in state i n times.
- Parameters
-
state The current state of the character. n The number of mutations to perform.
Implemented in bpp::AbstractMutationProcess.
The documentation for this class was generated from the following file:
- Bpp/Phyl/Simulation/MutationProcess.h
