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// File: NexusIOSequence.h
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// Created by: Julien Dutheil
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// Created on: Wed May 27 16:15 2009
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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 _NEXUSIOSEQUENCE_H_
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#define _NEXUSIOSEQUENCE_H_
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#include "AbstractISequence2.h"
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#include "../Sequence.h"
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#include "../Container/SequenceContainer.h"
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#include "../Container/VectorSequenceContainer.h"
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#include "../Container/AlignedSequenceContainer.h"
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* @brief The Nexus format reader for sequences.
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* An AlignedSequenceContainer is used instead of a VectorSequenceContainer.
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* This reader is not supposed to be a full parser of the Nexus files,
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* but only extract the sequence data. Only a basic subset of the options
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* are and will be supported.
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* This format is described in the following paper:
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* Maddison D, Swofford D, and Maddison W (1997), _Syst Biol_ 46(4):590-621
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* @author Julien Dutheil
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class NexusIOSequence:
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public AbstractIAlignment
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* @brief The maximum number of chars to be written on a line.
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unsigned int charsByLine_;
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* @brief Build a new Phylip file reader.
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* @param charsByLine The number of base to display in a row (ignored for now, no writing support).
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* @param checkSequenceNames Tell if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).
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NexusIOSequence(unsigned int charsByLine = 100, bool checkSequenceNames = true):
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charsByLine_(charsByLine), checkNames_(checkSequenceNames) {}
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virtual ~NexusIOSequence() {}
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* @name The AbstractISequence2 interface.
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void appendFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
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* @name The IOSequence interface.
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const std::string getFormatName() const;
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const std::string getFormatDescription() const;
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* @return true if the names are to be checked when reading sequences from files.
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bool checkNames() const { return checkNames_; }
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* @brief Tell whether the sequence names should be checked when reading from files.
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* @param yn whether the sequence names should be checked when reading from files.
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void checkNames(bool yn) { checkNames_ = yn; }
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const std::vector<std::string> splitNameAndSequence_(const std::string & s) const throw (Exception);
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} //end of namespace bpp.
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#endif //_NEXUSIOSEQUENCE_H_
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src/Bpp/Seq/Io/NexusIoSequence.h
