fastaParser.hpp

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/*
 * Copyright (c) 2023 Anthony J. Greenberg
 *
 * Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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 * 2. 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.
 *
 * 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
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 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND 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 THE COPYRIGHT HOLDER OR CONTRIBUTORS
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#pragma once
 
#include <vector>
#include <unordered_map>
#include <utility> // for std::pair
#include <string>
#include <iterator>
#include <cstdint>
 
namespace BayesicSpace {
    struct AlignmentStatistics;
    class ParseFASTA;
 
    struct AlignmentStatistics {
        size_t referenceStart;
        size_t referenceLength;
        size_t queryStart;
        size_t queryLength;
    };
    class ParseFASTA {
    public:
        ParseFASTA() = default;
        ParseFASTA(const std::string &fastaFileName);
        ParseFASTA(const ParseFASTA &toCopy);
        ParseFASTA(ParseFASTA &&toMove) noexcept;
        ParseFASTA& operator=(const ParseFASTA &toCopy);
        ParseFASTA& operator=(ParseFASTA &&toMove) noexcept;
        ~ParseFASTA() = default;
        size_t sequenceNumber() const noexcept {return fastaAlignment_.size(); };
        size_t alignmentLength() const {return fastaAlignment_.at(0).second.size(); };
        std::string extractConsensusWindow(const size_t &startIdx, const size_t &windowLength) const;
        std::vector< std::pair< size_t, std::vector<uint32_t> > > diversityInWindows(const size_t &windowSize, const size_t &stepSize) const;
        std::unordered_map<std::string, uint32_t> extractWindow(const size_t &windowStartPosition, const size_t &windowSize) const;
        std::vector< std::pair<std::string, uint32_t> > extractWindowSorted(const size_t &windowStartPosition, const size_t &windowSize) const;
        AlignmentStatistics extractSequence(const std::string &querySequence) const;
        void imputeMissing();
    private:
        std::vector< std::pair<std::string, std::string> > fastaAlignment_;
        std::string consensus_;
        void makeConsensus_();
    };
}