// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
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// Author: David Alexander

#pragma once

namespace ConsensusCore
{
    struct PoaParameterSet
    {
        float Extra;
        float Missing;
        float Mismatch;
        float Match;
        float Branch;

        static PoaParameterSet DefaultParameters();
    };

    struct PoaConfig
    {
        enum
        {
            GLOBAL_ALIGNMENT = false,
            LOCAL_ALIGNMENT = true
        };
        enum
        {
            USE_MERGE_MOVE = true,
            NO_MERGE_MOVE = false
        };

        PoaParameterSet Params;
        bool UseMergeMove;
        bool UseLocalAlignment;

        PoaConfig(PoaParameterSet params, bool useLocalAlignment, bool useMergeMove);
        PoaConfig(PoaParameterSet params, bool useLocalAlignment);
        explicit PoaConfig(bool useLocalAlignment);
        PoaConfig();

    private:
        void init(PoaParameterSet params, bool useLocalAlignment, bool useMergeMove);
    };
}
