externalFuncs.h File Reference

Define additional function information for call to user function when calculating the emission or transition value At a state the function may be called and passed information. The function may need traceback data or other sequence data. Such options are defined by the externalFuncs class. More...

#include <iostream>
#include <map>
#include <string>
#include <vector>
#include "weight.h"
#include "userFunctions.h"
#include "stochTypes.h"
#include "track.h"
#include "text.h"
#include "sequences.h"
#include <stdlib.h>

Go to the source code of this file.

Classes
class	StochHMM::transitionFuncParam
class	StochHMM::emissionFuncParam

Namespaces
namespace	StochHMM
	traceback_path.h

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Detailed Description

Define additional function information for call to user function when calculating the emission or transition value At a state the function may be called and passed information. The function may need traceback data or other sequence data. Such options are defined by the externalFuncs class.

User-provided weight can be passed to externalFuncs to weight the score when passing to emission or transition

Functions must be defined before model import, then will be passed to the externaFuncs class, when created.

Defined in the model definition files

See also:

userFunctions.h and userFunctions.cpp

Definition in file externalFuncs.h.