similarityMatrix.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.
 *
 * 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.
 *
 * 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
 * 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
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 */
 
 
#pragma once
 
#include <vector>
#include <array>
#include <string>
#include <cstdint>
#include <cstddef>
 
namespace BayesicSpace {
    struct RowColIdx;
    struct FullIdxValue;
    struct JaccardPair;
    struct DiffElementPair;
    struct FullIdxTrio;
    class SimilarityMatrix;
 
    struct RowColIdx {
        uint32_t iRow;
        uint32_t jCol;
    };
    struct FullIdxValue {
        uint64_t fullIdx;
        uint8_t quantSimilarity;
    };
    struct JaccardPair {
        uint64_t nIntersect;
        uint64_t nUnion;
    };
 
    void chunkedAppend(std::vector<uint64_t> &source, std::vector<uint64_t> &target);
    [[gnu::warn_unused_result]] RowColIdx recoverRCindexes(const uint64_t &vecIdx) noexcept;
 
    class SimilarityMatrix {
    public:
        SimilarityMatrix() noexcept  = default;
        SimilarityMatrix(const SimilarityMatrix &toCopy) = default;
        SimilarityMatrix& operator=(const SimilarityMatrix &toCopy) = default;
        SimilarityMatrix( SimilarityMatrix &&toMove) noexcept = default;
        SimilarityMatrix& operator=( SimilarityMatrix &&toMove) noexcept = default;
        ~SimilarityMatrix() = default;
 
        [[gnu::warn_unused_result]] static size_t elementSize() noexcept {return sizeof(uint64_t);};
        [[gnu::warn_unused_result]] size_t objectSize() const noexcept { 
            return  elementSize() * matrix_.size();
        };
        [[gnu::warn_unused_result]] size_t nElements() const noexcept {return matrix_.size();};
        void insert(const RowColIdx &rowColPair, const JaccardPair &jaccardCounts);
        void merge(SimilarityMatrix &toMerge);
        void save(const std::string &outFileName, const size_t &nThreads, const std::string &locusNameFile = "") const;
    private:
        std::vector<uint64_t> matrix_;
 
        // static members
        static const std::array<float, 256> floatLookUp_;
        static const std::array<const char*, 256> stringLookUp_;
        static const uint64_t maxIdxBitfield_;
        static const uint32_t maxRowColValue_;
        static const uint64_t valueMask_;
        static const uint64_t maxValueIdx_;
        static const uint64_t valueSize_;
        [[gnu::warn_unused_result]] static std::string stringify_(std::vector<uint64_t>::const_iterator start, std::vector<uint64_t>::const_iterator end,
                                const std::vector<std::string> &locusNames);
        void insert_(const FullIdxValue &indexWithSimilarity);
    };
}