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// Author: David Alexander
#pragma once
#include <boost/utility.hpp>
#include <climits>
#include <string>
#include <utility>
#include <vector>
#include <ConsensusCore/Align/AlignConfig.hpp>
#include <ConsensusCore/Poa/PoaGraph.hpp>
namespace ConsensusCore {
using boost::noncopyable;
class PoaGraph;
class PoaGraphPath;
class ScoredMutation;
AlignConfig DefaultPoaConfig(AlignMode mode = GLOBAL);
/// \brief A multi-sequence consensus obtained from a partial-order alignment
struct PoaConsensus : private noncopyable
{
const std::string Sequence;
PoaGraph Graph;
std::vector<PoaGraph::Vertex> Path;
PoaConsensus(const std::string& css, const PoaGraph& g,
const std::vector<PoaGraph::Vertex>& ConsensusPath);
// NB: this constructor exists to provide a means to avoid an unnecessary copy
// of the
// boost graph. If we had move semantics (C++11) we would be able to get by
// without
// this.
PoaConsensus(const std::string& css, const detail::PoaGraphImpl& g,
const std::vector<PoaGraph::Vertex>& ConsensusPath);
~PoaConsensus();
static const PoaConsensus* FindConsensus(const std::vector<std::string>& reads);
static const PoaConsensus* FindConsensus(const std::vector<std::string>& reads,
const AlignConfig& config, int minCoverage = -INT_MAX);
static const PoaConsensus* FindConsensus(const std::vector<std::string>& reads, AlignMode mode,
int minCoverage = -INT_MAX);
public:
// Additional accessors, which do things on the graph/graphImpl
// LikelyVariants
public:
std::string ToGraphViz(int flags = 0) const;
void WriteGraphVizFile(std::string filename, int flags = 0) const;
};
}
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