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//***************************************************************************
//* Copyright (c) 2016 Saint Petersburg State University
//* All Rights Reserved
//* See file LICENSE for details.
//***************************************************************************
#ifndef __KMER_MAP_HPP__
#define __KMER_MAP_HPP__
#include "sequence/rtseq.hpp"
#include <hat-trie/hat-trie.h>
#include <boost/iterator/iterator_facade.hpp>
namespace debruijn_graph {
class KMerMap {
typedef RtSeq Kmer;
typedef RtSeq Seq;
typedef typename Seq::DataType RawSeqData;
value_t* internal_tryget(const Kmer &key) const {
return hattrie_tryget(mapping_, (const char *)key.data(), rawcnt_ * sizeof(RawSeqData));
}
value_t* internal_get(const Kmer &key) const {
return hattrie_get(mapping_, (const char *)key.data(), rawcnt_ * sizeof(RawSeqData));
}
int internal_erase(const Kmer &key) {
return hattrie_del(mapping_, (const char *)key.data(), rawcnt_ * sizeof(RawSeqData));
}
class iterator : public boost::iterator_facade<iterator,
const std::pair<Kmer, Seq>,
std::forward_iterator_tag,
const std::pair<Kmer, Seq>> {
public:
iterator(unsigned k, hattrie_iter_t *start = nullptr)
: k_(k), iter_(start, [](hattrie_iter_t *p) { hattrie_iter_free(p); }) {}
private:
friend class boost::iterator_core_access;
void increment() {
hattrie_iter_next(iter_.get());
}
bool equal(const iterator &other) const {
// Special case: NULL and finished are equal
if (iter_.get() == nullptr || hattrie_iter_finished(iter_.get()))
return other.iter_.get() == nullptr || hattrie_iter_finished(other.iter_.get());
if (other.iter_.get() == nullptr)
return false;
return hattrie_iter_equal(iter_.get(), other.iter_.get());
}
const std::pair<Kmer, Seq> dereference() const {
size_t len;
Kmer k(k_, (const RawSeqData*)hattrie_iter_key(iter_.get(), &len));
Seq s(k_, (const RawSeqData*)(*hattrie_iter_val(iter_.get())));
return std::make_pair(k, s);
}
unsigned k_;
std::shared_ptr<hattrie_iter_t> iter_;
};
public:
KMerMap(unsigned k)
: k_(k), mapping_(hattrie_create()) {
rawcnt_ = (unsigned)Seq::GetDataSize(k_);
}
~KMerMap() {
clear();
hattrie_free(mapping_);
}
void erase(const Kmer &key) {
value_t *vp = internal_tryget(key);
if (vp == nullptr)
return;
RawSeqData *value = reinterpret_cast<RawSeqData*>(*vp);
delete[] value;
int res = internal_erase(key);
VERIFY_MSG(res == 0, "Failed to delete from kmer mapper");
}
void set(const Kmer &key, const Seq &value) {
value_t *vp = internal_tryget(key);
RawSeqData *rawvalue = nullptr;
if (vp == nullptr) {
vp = internal_get(key);
rawvalue = new RawSeqData[rawcnt_];
*vp = reinterpret_cast<uintptr_t>(rawvalue);
} else {
rawvalue = reinterpret_cast<RawSeqData*>(*vp);
}
memcpy(rawvalue, value.data(), rawcnt_ * sizeof(RawSeqData));
}
bool count(const Kmer &key) const {
return internal_tryget(key) != nullptr;
}
const RawSeqData *find(const Kmer &key) const {
value_t *vp = internal_tryget(key);
if (vp == nullptr)
return nullptr;
return reinterpret_cast<const RawSeqData*>(*vp);
}
void clear() {
// Delete all the values
auto *iter = hattrie_iter_begin(mapping_, false);
while (!hattrie_iter_finished(iter)) {
RawSeqData *value = (RawSeqData*)(*hattrie_iter_val(iter));
delete[] value;
hattrie_iter_next(iter);
}
hattrie_iter_free(iter);
// Delete the mapping and all the keys
hattrie_clear(mapping_);
}
size_t size() const {
return hattrie_size(mapping_);
}
iterator begin() const {
return iterator(k_, hattrie_iter_begin(mapping_, false));
}
iterator end() const {
return iterator(k_);
}
private:
unsigned k_;
unsigned rawcnt_;
hattrie_t *mapping_;
};
}
#endif // __KMER_MAP_HPP__
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