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// Author: David Alexander
#pragma once
#include <boost/tuple/tuple.hpp>
#include <climits>
#include <string>
#include <utility>
#include <vector>
#include <ConsensusCore/Mutation.hpp>
#include <ConsensusCore/Types.hpp>
namespace ConsensusCore {
struct PoaConsensus;
namespace detail {
class PoaGraphImpl;
}
class PoaAlignmentMatrix
{
public:
virtual ~PoaAlignmentMatrix(){};
virtual float Score() const = 0;
};
/// \brief An object representing a Poa (partial-order alignment) graph
class PoaGraph
{
public:
typedef size_t Vertex;
typedef size_t ReadId;
public: // Flags enums for specifying GraphViz output features
enum
{
COLOR_NODES = 0x1,
VERBOSE_NODES = 0x2
};
public:
PoaGraph();
PoaGraph(const PoaGraph& other);
PoaGraph(const detail::PoaGraphImpl& o); // NB: this performs a copy
~PoaGraph();
//
// Easy API
//
void AddRead(const std::string& sequence, const AlignConfig& config,
detail::SdpRangeFinder* rangeFinder = NULL,
std::vector<Vertex>* readPathOutput = NULL);
//
// API for more control
//
void AddFirstRead(const std::string& sequence, std::vector<Vertex>* readPathOutput = NULL);
PoaAlignmentMatrix* TryAddRead(const std::string& sequence, const AlignConfig& config,
detail::SdpRangeFinder* rangeFinder = NULL) const;
void CommitAdd(PoaAlignmentMatrix* mat, std::vector<Vertex>* readPathOutput = NULL);
// ----------
size_t NumReads() const;
std::string ToGraphViz(int flags = 0, const PoaConsensus* pc = NULL) const;
void WriteGraphVizFile(std::string filename, int flags = 0,
const PoaConsensus* pc = NULL) const;
const PoaConsensus* FindConsensus(const AlignConfig& config, int minCoverage = -INT_MAX) const;
private:
detail::PoaGraphImpl* impl;
};
}
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