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/* This file is part of Jellyfish.
Jellyfish is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Jellyfish is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Jellyfish. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __SEQUENCE_MERS_H__
#define __SEQUENCE_MERS_H__
#include <iterator>
#include <jellyfish/mer_dna.hpp>
class sequence_mers : public std::iterator<std::input_iterator_tag, jellyfish::mer_dna> {
public:
typedef jellyfish::mer_dna mer_type;
private:
const char* cseq_;
const char* eseq_;
const bool canonical_;
unsigned int filled_;
mer_type m_; // mer
mer_type rcm_; // reverse complement mer
public:
explicit sequence_mers(bool canonical = false) :
cseq_(0), eseq_(0), canonical_(canonical), filled_(0)
{ }
sequence_mers(const sequence_mers& rhs) :
cseq_(rhs.cseq_), eseq_(rhs.eseq_), canonical_(rhs.canonical_), filled_(rhs.filled_),
m_(rhs.m_), rcm_(rhs.rcm_)
{ }
sequence_mers(sequence_mers&& rhs) :
cseq_(rhs.cseq_), eseq_(rhs.eseq_), canonical_(rhs.canonical_), filled_(rhs.filled_),
m_(std::move(rhs.m_)), rcm_(std::move(rcm_))
{ }
void reset(const char* seq, const char* seqe) {
cseq_ = seq;
eseq_ = seqe;
filled_ = 0;
this->operator++();
}
sequence_mers& operator=(const std::string& seq) {
reset(seq.c_str(), seq.c_str() + seq.size());
return *this;
}
sequence_mers& operator=(const char* seq) {
reset(seq, seq + strlen(seq));
return *this;
}
bool operator==(const sequence_mers& rhs) const { return cseq_ == rhs.cseq_; }
bool operator!=(const sequence_mers& rhs) const { return cseq_ != rhs.cseq_; }
operator void*() const { return (void*)cseq_; }
const mer_type& operator*() const { return !canonical_ || m_ < rcm_ ? m_ : rcm_; }
const mer_type* operator->() const { return &this->operator*(); }
sequence_mers& operator++() {
if(cseq_ >= eseq_) {
cseq_ = eseq_ = 0;
return *this;
}
do {
int code = m_.code(*cseq_++);
if(code >= 0) {
m_.shift_left(code);
if(canonical_)
rcm_.shift_right(rcm_.complement(code));
filled_ = std::min(filled_ + 1, jellyfish::mer_dna::k());
} else
filled_ = 0;
} while(filled_ < jellyfish::mer_dna::k() && cseq_ < eseq_);
return *this;
}
sequence_mers operator++(int) {
sequence_mers res(*this);
++*this;
return res;
}
};
#endif /* __SEQUENCE_MERS_H__ */
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