HMM classes

[renatocf]

Join HMM, GHMM and profile-HMM in a single class based on GHMM.

[renatocf]

Tasks:

• Simplify State template hierarchy (State, StateCrtp, SimpleState, DurationState) to a single non-template class State.
• Receive ProbabilisticModelPtr emission / transition in State constructor.
• Receive Duration strategy element in State constructor.
• Move methods related to states from DecodableModelCrtp to new GHMM class.
• Move methods related to alphabet size from DecodableModelCrtp to new GHMM class.
• Remove struct StateTraits.
• Remove file HiddenMarkovModelState.hpp.
• Remove file GeneralizedHiddenMarkovModelState.hpp.
• Merge HMM and GHMM algorithms.
• Create static method makeHMM to create a HMM from new GHMM class.
• Create static method makeProfileHMM to create a Profile-HMM from new GHMM class.
• Create tags for HMM, ProfileHMM and GHMM training algorithms.
• Remove files HiddenMarkovModel.hpp and HiddenMarkovModel.cpp.
• Think about joining HMM / GHMM tests.
• Create tests for ProfileHMM.
• Fix model::Translator visitor to use new GHMM::State.
• Fix helper::SExprTranslator visitor to test new GHMM::State serialization.
• Fix style accordingly to make style-lint.
• Fix static errors accordingly to make analysis-lint.