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// File: SubstitutionModelSetTools.h
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// Created by: Julien Dutheil
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// Created on: tue Sep 17 16:57 2007
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Copyright or © or Copr. CNRS, (November 16, 2004)
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This software is a computer program whose purpose is to provide classes
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for phylogenetic data analysis.
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This software is governed by the CeCILL license under French law and
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abiding by the rules of distribution of free software. You can use,
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modify and/ or redistribute the software under the terms of the CeCILL
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license as circulated by CEA, CNRS and INRIA at the following URL
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"http://www.cecill.info".
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As a counterpart to the access to the source code and rights to copy,
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modify and redistribute granted by the license, users are provided only
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with a limited warranty and the software's author, the holder of the
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economic rights, and the successive licensors have only limited
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In this respect, the user's attention is drawn to the risks associated
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with loading, using, modifying and/or developing or reproducing the
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software by the user in light of its specific status of free software,
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that may mean that it is complicated to manipulate, and that also
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therefore means that it is reserved for developers and experienced
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professionals having in-depth computer knowledge. Users are therefore
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encouraged to load and test the software's suitability as regards their
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requirements in conditions enabling the security of their systems and/or
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data to be ensured and, more generally, to use and operate it in the
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same conditions as regards security.
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The fact that you are presently reading this means that you have had
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knowledge of the CeCILL license and that you accept its terms.
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#ifndef _SUBSTITUTIONMODELSETTOOLS_H_
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#define _SUBSTITUTIONMODELSETTOOLS_H_
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#include "SubstitutionModelSet.h"
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* @brief Tools for automatically creating SubstitutionModelSet objects.
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class SubstitutionModelSetTools
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* @brief Create a SubstitutionModelSet object, corresponding to the homogeneous case.
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* This class is mainly for testing purpose.
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* @param model The model to use.
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* @param rootFreqs A FrequenciesSet object to parametrize root frequencies.
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* @param tree The tree to use for the construction of the set.
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static SubstitutionModelSet* createHomogeneousModelSet(
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SubstitutionModel* model,
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FrequenciesSet* rootFreqs,
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) throw (AlphabetException, Exception);
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* @brief Create a SubstitutionModelSet object, with one model per branch.
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* All branches share the same type of model, but allow one set of parameters per branch.
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* This is also possible to specify some parameters to be common to all branches.
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* @param model The model to use.
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* @param rootFreqs A FrequenciesSet object to parametrize root frequencies.
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* @param tree The tree to use for the construction of the set.
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* @param globalParameterNames Common parameters for all branches.
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* All other parameters will be considered distinct for all branches.
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static SubstitutionModelSet* createNonHomogeneousModelSet(
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SubstitutionModel* model,
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FrequenciesSet* rootFreqs,
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const std::vector<std::string>& globalParameterNames
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) throw (AlphabetException, Exception);
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} //end of namespace bpp.
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#endif //_SUBSTITUTIONMODELSETTOOLS_H_
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src/Bpp/Phyl/Model/SubstitutionModelSetTools.h
