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// File: AlphabetIndex2.h
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// Created by: Julien Dutheil
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// Created on: Mon Feb 21 17:42 2005
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Copyright or © or Copr. CNRS, (November 17, 2004)
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This software is a computer program whose purpose is to provide classes
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for sequences 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 _ALPHABETINDEX2_H_
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#define _ALPHABETINDEX2_H_
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#include "../Alphabet/Alphabet.h"
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#include <Bpp/Clonable.h>
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#include <Bpp/Numeric/Matrix/Matrix.h>
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* @brief Two dimensionnal alphabet index interface.
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* Derivatives of this interface implement distances between two states.
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class AlphabetIndex2: public Clonable
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virtual ~AlphabetIndex2() {}
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* @brief Get the index associated to a pair of states.
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* @param state1 First state to consider, as a int value.
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* @param state2 Second state to consider, as a int value.
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* @return The index associated to the pair of states
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virtual T getIndex(int state1, int state2) const = 0;
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* @brief Get the index associated to a pair of states.
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* @param state1 First state to consider, as a string value.
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* @param state2 Second state to consider, as a string value.
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* @return The index associated to the pair of states
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virtual T getIndex(const std::string& state1, const std::string& state2) const = 0;
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* @brief Get the alphabet associated to this index.
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* @return Alphabet The alphabet associated to this index.
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virtual const Alphabet* getAlphabet() const = 0;
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* @return A matrix object with all indices.
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virtual Matrix<T>* getIndexMatrix() const = 0;
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} //end of namespace bpp.
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#endif //_ALPHABETINDEX2_H_
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src/Bpp/Seq/StateProperties/AlphabetIndex2.h
