40 #ifndef _IOSUBSTITUTIONMODEL_H_ 41 #define _IOSUBSTITUTIONMODEL_H_ 43 #include "../Model/SubstitutionModel.h" 46 #include <Bpp/Exceptions.h> 47 #include <Bpp/Io/IoFormat.h> 48 #include <Bpp/Io/OutputStream.h> 51 #include <Bpp/Seq/Container/SiteContainer.h> 56 class SubstitutionModel;
62 public virtual IOFormat
69 virtual const std::string
getDataType()
const {
return "Substitution Model"; }
95 const std::string& modelDescription,
96 const SiteContainer* data = 0,
97 bool parseArguments =
true) = 0;
130 std::map<std::string, std::string>& globalAliases,
131 std::vector<std::string>& writtenNames)
const = 0;
137 #endif //_IOSUBSTITUTIONMODEL_H_ Interface for all substitution models.
virtual ~ISubstitutionModel()
virtual void write(const SubstitutionModel &model, OutputStream &out, std::map< std::string, std::string > &globalAliases, std::vector< std::string > &writtenNames) const =0
Write a substitution model to a stream.
General interface for distance matrix readers.
General interface for distance matrix writers.
virtual ~OSubstitutionModel()
virtual const std::string getDataType() const
virtual const std::map< std::string, std::string > & getUnparsedArguments() const =0
virtual ~IoSubstitutionModel()
General interface for model I/O.
virtual SubstitutionModel * read(const Alphabet *alphabet, const std::string &modelDescription, const SiteContainer *data=0, bool parseArguments=true)=0
Read a substitution model from a string.