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// Created by: Sylvain Gaillard
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// Created on: Wed Nov 5 2008
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Copyright or © or Copr. CNRS, (November 5, 2008)
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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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#include "ISequenceStream.h"
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#include "../Sequence.h"
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#include "../SequenceWithQuality.h"
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* @brief The phd sequence file format from phred software.
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* This class read DNA SequenceWithQuality from phd files produced by the
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* phred program from the University of Washington.
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* // Creating a SequenceWithQuality object
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* SequenceWithQuality seq(&alpha);
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* std::vector<int> pos;
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* // Create a PhredPhd parser
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* std::ifstream in("my_sequence.phd");
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* // Read the sequence
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* pp.nextSequence(in, seq, pos);
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* @author Sylvain Gaillard
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class PhredPhd: public ISequenceStream {
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* @brief Build a new PhredPhd object.
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virtual ~PhredPhd() {}
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* @name The ISequenceStream interface.
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) const throw (Exception);
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* @brief Read a SequenceWithQuality from stream
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SequenceWithQuality& seq
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) const throw (Exception);
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* @brief Read a SequenceWithQuality from stream and store chromatographic positions
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* A more complete parser that read a SequenceWithQuality and store
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* the position of each base call on the chromatogram in a vector of
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* @param input The stram to read.
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* @param seq The sequence to fill.
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* @param pos The vector of positions to fill.
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* @throw Exception IOException and Sequence related exceptions.
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SequenceWithQuality& seq,
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std::vector<int>& pos
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) const throw (Exception);
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* @name The IOFormat interface.
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const std::string getDataType() const { return "SequenceWithQuality"; };
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const std::string getFormatName() const { return "phd file"; };
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const std::string getFormatDescription() const {
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return "Sequences following the phd format as describe in the phred documentation.";
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* @brief Global file parser
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* @param input The stream to read
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* @param name The string to store the sequence name
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* @param sequence The string to store the sequence
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* @param qual The vector to store qualities
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* @param pos The vector to store positions
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void parseFile_(std::istream& input, std::string& name, std::string& sequence, std::vector<int>& qual, std::vector<int>& pos) const;
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* @brief Parse the DNA part of the file
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* Read the DNA part until `END_DNA' or EOF.
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* @param input The stream to read
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* @param sequence The string to store the sequence
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* @param qual The vector to store qualities
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* @param pos The vector to store positions
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void parseDNA_(std::istream& input, std::string& sequence, std::vector<int>& qual, std::vector<int>& pos) const;
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} //end of namespace bpp
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#endif // _PHREDPHD_H_
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src/Bpp/Seq/Io/PhredPhd.h
