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// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
//
// * Neither the name of Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
// Author: David Alexander
#pragma once
#include <boost/utility.hpp>
#include <string>
#include <utility>
#include <vector>
#include "PoaConfig.hpp"
#include "PoaGraph.hpp"
namespace ConsensusCore
{
using boost::noncopyable;
/// \brief A multi-sequence consensus obtained from a partial-order alignment
class PoaConsensus : private noncopyable
{
std::string consensusSequence_;
PoaConfig config_;
std::vector< std::pair<Mutation*, float> >* variants_;
PoaGraph* poaGraph_;
float score_;
public:
explicit PoaConsensus(const PoaConfig& config);
~PoaConsensus();
public:
static const PoaConsensus* FindConsensus(const std::vector<std::string>& reads,
const PoaConfig& config);
static const PoaConsensus* FindConsensus(const std::vector<std::string>& reads,
bool global);
static const PoaConsensus* FindConsensus(const std::vector<std::string>& reads);
public:
const PoaGraph* Graph() const;
float Score() const;
// Consensus interface methods
std::string Sequence() const;
std::string ToString() const;
// Mutations interface
const std::vector< std::pair<Mutation*, float> >* Mutations() const;
};
}
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