45 #include <Bpp/Numeric/Matrix/Matrix.h> 47 #include <Bpp/Numeric/ParameterList.h> 49 #include <Bpp/Seq/Alphabet/ProteicAlphabet.h> 50 #include <Bpp/Seq/Container/SequenceContainer.h> 78 CoalaCore(
size_t nbAxes = 0,
const std::string& exch =
"LG08");
92 ParameterList
computeCOA(
const SequenceContainer& data,
bool param =
true);
94 std::vector<double>
prodMatrixVector(RowMatrix<double>& P, std::vector<double>& V);
99 #endif // _COALACORE_H_
size_t getNbrOfAxes() const
std::vector< double > colWeights_
const std::vector< double > & getColumnWeights() const
std::vector< double > prodMatrixVector(RowMatrix< double > &P, std::vector< double > &V)
CoalaCore(size_t nbAxes=0, const std::string &exch="LG08")
const RowMatrix< double > & getTppalAxesMatrix() const
ParameterList computeCOA(const SequenceContainer &data, bool param=true)
CoalaCore * clone() const
void setParamValues(const std::map< std::string, std::string > &valuesSettings)
This class is the core class inherited by the Coala class. COaLA is a branch-heterogeneous amino-acid...
std::map< std::string, std::string > paramValues_
const RowMatrix< double > & getRowCoordinates() const