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pkmer_t.hpp
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pkmer_t.hpp
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#pragma once
#include "packing.hpp"
struct pkmer_t {
unsigned char data[PACKED_KMER_LEN];
// Get the k-kmer string, hash the k-mer.
std::string get() const noexcept;
uint64_t hash() const noexcept;
// Various C++ lifetime stuff.
pkmer_t(const std::string &kmer);
pkmer_t(const pkmer_t &pkmer);
pkmer_t() {}
pkmer_t operator=(const pkmer_t &pkmer);
bool operator==(const pkmer_t &pkmer) const noexcept;
bool operator!=(const pkmer_t &pkmer) const noexcept;
void init(const unsigned char data[PACKED_KMER_LEN]);
};
std::string pkmer_t::get() const noexcept {
char kmer[KMER_LEN];
unpackKmer(data, kmer);
return std::string(kmer, KMER_LEN);
}
uint64_t pkmer_t::hash() const noexcept {
unsigned long hashval = 5381;
for (int i = 0; i < PACKED_KMER_LEN; i++) {
hashval = data[i] + (hashval << 5) + hashval;
}
return hashval;
}
pkmer_t::pkmer_t(const std::string &kmer) {
packKmer(kmer.data(), data);
}
pkmer_t::pkmer_t(const pkmer_t &pkmer) {
init(pkmer.data);
}
pkmer_t pkmer_t::operator=(const pkmer_t &pkmer) {
init(pkmer.data);
}
bool pkmer_t::operator==(const pkmer_t &pkmer) const noexcept {
return memcmp(pkmer.data, data, PACKED_KMER_LEN) == 0;
}
bool pkmer_t::operator!=(const pkmer_t &pkmer) const noexcept {
return !(*this == pkmer);
}
void pkmer_t::init(const unsigned char data[PACKED_KMER_LEN]) {
for (int i = 0; i < PACKED_KMER_LEN; i++) {
this->data[i] = data[i];
}
}