5 #ifndef BPP_PHYL_IO_BPPOSUBSTITUTIONMODELFORMAT_H
6 #define BPP_PHYL_IO_BPPOSUBSTITUTIONMODELFORMAT_H
10 #include "../Model/MixedTransitionModel.h"
29 static unsigned char DNA;
30 static unsigned char RNA;
37 static unsigned char ALL;
113 std::shared_ptr<const Alphabet> alphabet,
114 const std::string& modelDescription,
115 const std::map<
size_t, std::shared_ptr<const AlignmentDataInterface>>& mData,
117 bool parseArguments =
true)
override;
137 std::map<std::string, std::string>& globalAliases,
138 std::vector<std::string>& writtenNames)
const override;
143 std::unique_ptr<SubstitutionModelInterface>
readWord_(
144 std::shared_ptr<const Alphabet> alphabet,
145 const std::string& modelDescription,
146 const std::map<
size_t, std::shared_ptr<const AlignmentDataInterface>>& mData,
151 std::map<std::string, std::string>& globalAliases,
152 std::vector<std::string>& writtenNames)
const;
160 std::map<std::string, std::string>& args);
178 std::shared_ptr<const AlignmentDataInterface> data);
Interface for all Branch models.
General interface for model readers.
Interface for Transition models, defined as a mixture of "simple" transition models.
General interface for distance matrix writers.
Defines the basic types of data flow nodes.