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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 <vector>
#include <string>
#include <utility>
#include <tuple>
#include "ConsensusCore/Types.hpp"
#include "ConsensusCore/Mutation.hpp"
namespace ConsensusCore
{
/// \brief An object representing a Poa (partial-order alignment) graph
class PoaGraph
{
class Impl;
Impl* impl;
public: // Flags enums for specifying GraphViz output features
enum {
COLOR_NODES = 0x1,
VERBOSE_NODES = 0x2
};
public:
void AddSequence(const std::string& sequence, const PoaConfig& config);
// TODO(dalexander): move this method to PoaConsensus so we don't have to use a tuple
// interface here (which was done to avoid a circular dep on PoaConsensus).
#ifndef SWIG
std::tuple<std::string, float, std::vector< std::pair<Mutation*, float> >* >
FindConsensus(const PoaConfig& config) const;
#endif // !SWIG
int NumSequences() const;
std::string ToGraphViz(int flags = 0) const;
void WriteGraphVizFile(std::string filename, int flags = 0) const;
PoaGraph();
~PoaGraph();
};
}
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