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// File: AlphabetState.h
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// Author: Sylvain Gaillard
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// Created: 29/07/2009 13:56:01
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Copyright or © or Copr. CNRS, (July 29, 2009)
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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 _ALPHABETSTATE_H_
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#define _ALPHABETSTATE_H_
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#include <Bpp/Clonable.h>
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* @brief This is the base class to describe states in an Alphabet.
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* @author Sylvain Gaillard
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class AlphabetState: public virtual Clonable {
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AlphabetState(int num, const std::string& letter, const std::string& name): num_(num), letter_(letter), name_(name) {}
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virtual ~AlphabetState() {}
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* @name The Clonable interface.
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clone() const { return new AlphabetState(* this); }
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* @brief Get the state's number.
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* @return The state's number (i.e. -1 for gap (-)).
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int getNum() const { return num_; }
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* @brief Set the state's number.
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* @param num The state's number.
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void setNum(int num) { num_ = num; }
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* @brief Get the letter(s) corresponding to the state.
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* The letter is a string because it may more than one char
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* (for instance: codon).
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* @return The state's letter.
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const std::string& getLetter() const { return letter_; }
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* @brief Set the letter(s) of the state.
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* @param letter The state's letter.
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void setLetter(const std::string& letter) { letter_ = letter; }
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* @brief Get the name of the state.
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* @return The full name of the state (i.e. Adenine).
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const std::string& getName() const { return name_; }
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* @brief Set the name of the state.
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* @param name The state's name
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void setName(const std::string& name) { name_ = name; }
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* Comparison is done on state num
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bool operator == (AlphabetState& l2) {
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return getNum() == l2.getNum();
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#endif // _ALPHABETSTATE_H_
added
removed
src/Bpp/Seq/Alphabet/AlphabetState.h
