kmer_t.hpp

#pragma once

#include "packing.hpp"
#include "pkmer_t.hpp"

struct kmer_pair {
    pkmer_t kmer;
    char fb_ext[2];

    // Return the k-mer as a string
    std::string kmer_str() const noexcept;
    // Return the forward and backward extension as a string
    std::string fb_ext_str() const noexcept;

    // Return the next, previous kmer
    pkmer_t next_kmer() const noexcept;
    pkmer_t last_kmer() const noexcept;

    // Get the forward, backward extension.
    char forwardExt() const noexcept;
    char backwardExt() const noexcept;

    // Print the k-mer/fb_ext to STDOUT.
    void print() const noexcept;

    uint64_t hash() const noexcept;

    kmer_pair(const std::string& kmer, const std::string& fb_ext);

    kmer_pair() = default;
    ~kmer_pair() = default;

    kmer_pair(const kmer_pair& kmer) = default;
    kmer_pair& operator=(const kmer_pair& kmer) = default;

    void init(const std::string& kmer, const std::string& fb_ext);
    void init(const kmer_pair& kmer);

    bool operator==(const kmer_pair& kmer) const noexcept;
    bool operator!=(const kmer_pair& kmer) const noexcept;
};

char kmer_pair::forwardExt() const noexcept { return fb_ext[1]; }

char kmer_pair::backwardExt() const noexcept { return fb_ext[0]; }

std::string kmer_pair::kmer_str() const noexcept { return kmer.get(); }

std::string kmer_pair::fb_ext_str() const noexcept { return std::string(fb_ext, 2); }

pkmer_t kmer_pair::next_kmer() const noexcept {
    return pkmer_t(kmer_str().substr(1, std::string::npos) + forwardExt());
}

pkmer_t kmer_pair::last_kmer() const noexcept {
    return pkmer_t(backwardExt() + kmer_str().substr(0, kmer_str().length() - 1));
}

void kmer_pair::print() const noexcept {
    printf("%s %s\n", kmer_str().c_str(), fb_ext_str().c_str());
}

uint64_t kmer_pair::hash() const noexcept { return kmer.hash(); }

kmer_pair::kmer_pair(const std::string& kmer, const std::string& fb_ext) { init(kmer, fb_ext); }

void kmer_pair::init(const std::string& kmer, const std::string& fb_ext) {
    if (kmer.length() != KMER_LEN || fb_ext.length() != 2) {
        fprintf(stderr, "error: tried to initialize a kmer pair with too short a string.\n");
        return;
    }
    this->kmer = pkmer_t(kmer);
    for (int i = 0; i < 2; i++) {
        this->fb_ext[i] = fb_ext[i];
    }
}

bool kmer_pair::operator==(const kmer_pair& kmer) const noexcept {
    return kmer.kmer == this->kmer && fb_ext[0] == kmer.fb_ext[0] && fb_ext[1] == kmer.fb_ext[1];
}

bool kmer_pair::operator!=(const kmer_pair& kmer) const noexcept { return !(kmer == *this); }