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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2017, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
// This file is part of Lambda.
//
// Lambda is Free Software: you can redistribute it and/or modify it
// under the terms found in the LICENSE[.md|.rst] file distributed
// together with this file.
//
// Lambda 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.
//
// ==========================================================================
// match.h: Main File for the match class
// ==========================================================================
#ifndef SEQAN_LAMBDA_FINDER_H_
#define SEQAN_LAMBDA_FINDER_H_
// #include <forward_list>
// #include <unordered_map>
#include <vector>
#include "options.hpp"
using namespace seqan;
//-----------------------------------------------------------------------------
// Finder
//-----------------------------------------------------------------------------
template<typename TAlph>
struct Match
{
typedef SizeTypeNum_<TAlph> TQId;
typedef SizeTypeNum_<TAlph> TSId;
typedef SizeTypePos_<TAlph> TPos;
TQId qryId;
TSId subjId;
TPos qryStart;
// TPos qryEnd;
TPos subjStart;
// TPos subjEnd;
// Match()
// :
// qryId(0), qryStart(0), /*qryEnd(0),*/ subjId(0), subjStart(0)/*, subjEnd(0)*/
// {
// }
//
// Match(Match const & m2)
// {
// qryId = m2.qryId;
// qryStart = m2.qryStart;
// /*qryEnd = m2.qryEnd;*/
// subjId = m2.subjId;
// subjStart = m2.subjStart;
// /*subjEnd = m2.subjEnd;*/
// }
inline bool operator== (Match const & m2) const
{
return std::tie(qryId, subjId, qryStart, subjStart/*, qryEnd, subjEnd*/)
== std::tie(m2.qryId, m2.subjId, m2.qryStart, m2.subjStart/*, m2.qryEnd, m2.subjEnd*/);
}
inline bool operator< (Match const & m2) const
{
return std::tie(qryId, subjId, qryStart, subjStart/*, qryEnd, subjEnd*/)
< std::tie(m2.qryId, m2.subjId, m2.qryStart, m2.subjStart/*, m2.qryEnd, m2.subjEnd*/);
}
};
template <typename TAlph>
inline void
setToSkip(Match<TAlph> & m)
{
using TPos = typename Match<TAlph>::TPos;
constexpr TPos posMax = std::numeric_limits<TPos>::max();
m.qryStart = posMax;
m.subjStart = posMax;
}
template <typename TAlph>
inline bool
isSetToSkip(Match<TAlph> const & m)
{
using TPos = typename Match<TAlph>::TPos;
constexpr TPos posMax = std::numeric_limits<TPos>::max();
return (m.qryStart == posMax) && (m.subjStart == posMax);
}
// struct IdPairHash
// {
// std::size_t
// operator()(std::pair<Match::TQId, Match::TSId> const & pair) const
// {
// return std::hash<Match::TQId>()(std::get<0>(pair)) ^
// std::hash<Match::TSId>()(std::get<1>(pair));
// }
// };
//
//
// // this is a comparison structure that takes the relative abundance of hits
// // on a specific subject into account thereby moving those subjects to
// // front of a queries hits that are more likely to be top-scoring
// struct MatchSortComp :
// public ::std::binary_function <Match, Match, bool>
// {
// std::unordered_map<std::pair<Match::TQId, Match::TSId>,
// uint64_t,
// IdPairHash> map;
//
// MatchSortComp(std::vector<Match> const & matches)
// {
// for (Match const & m : matches)
// ++map[std::make_pair(m.qryId, m.subjId)];
// }
//
// inline bool operator() (Match const & i, Match const & j) const
// {
// int64_t iAb = -map.at(std::make_pair(i.qryId, i.subjId));
// int64_t jAb = -map.at(std::make_pair(j.qryId, j.subjId));
// return std::tie(i.qryId,
// iAb,
// i.qryStart,
// i.subjStart)
// < std::tie(j.qryId,
// jAb,
// j.qryStart,
// j.subjStart);
// }
// };
template <typename TGH, typename TAlph>
inline void
myHyperSortSingleIndex(std::vector<Match<TAlph>> & matches,
bool const doubleIndexing,
TGH const &)
{
using TId = typename Match<TAlph>::TQId;
// regular sort
std::sort(matches.begin(), matches.end());
// trueQryId, begin, end
std::vector<std::tuple<TId, TId, TId>> intervals;
for (TId i = 1; i <= length(matches); ++i)
{
if ((i == length(matches)) ||
(matches[i-1].qryId != matches[i].qryId) ||
(matches[i-1].subjId / sNumFrames(TGH::blastProgram)) !=
(matches[i].subjId / sNumFrames(TGH::blastProgram)))
{
if (length(intervals) == 0) // first interval
intervals.emplace_back(std::make_tuple(matches[i-1].qryId
/ qNumFrames(TGH::blastProgram),
0,
i));
else
intervals.emplace_back(std::make_tuple(matches[i-1].qryId
/ qNumFrames(TGH::blastProgram),
std::get<2>(intervals.back()),
i));
}
}
if (doubleIndexing)
{
// sort by trueQryId, then lengths of interval
std::sort(intervals.begin(), intervals.end(),
[] (std::tuple<TId, TId, TId> const & i1,
std::tuple<TId, TId, TId> const & i2)
{
return (std::get<0>(i1) != std::get<0>(i2))
? (std::get<0>(i1) < std::get<0>(i2))
: ((std::get<2>(i1) - std::get<1>(i1))
> (std::get<2>(i2) - std::get<1>(i2)));
});
} else
{
// sort by lengths of interval, since trueQryId is the same anyway
std::sort(intervals.begin(), intervals.end(),
[] (std::tuple<TId, TId, TId> const & i1,
std::tuple<TId, TId, TId> const & i2)
{
return (std::get<2>(i1) - std::get<1>(i1))
> (std::get<2>(i2) - std::get<1>(i2));
});
}
std::vector<Match<TAlph>> tmpVector;
tmpVector.resize(matches.size());
TId newIndex = 0;
for (auto const & i : intervals)
{
TId limit = std::get<2>(i);
for (TId j = std::get<1>(i); j < limit; ++j)
{
tmpVector[newIndex] = matches[j];
newIndex++;
}
}
std::swap(tmpVector, matches);
}
// inline bool
// overlap(Match const & m1, Match const & m2, unsigned char d = 0)
// {
// SEQAN_ASSERT_EQ(m1.qryId, m2.qryId);
// SEQAN_ASSERT_EQ(m1.subjId, m2.subjId);
//
// // if ( //match beginnings overlap
// // ((m1.qryStart >= _protectUnderflow(m2.qryStart, d)) &&
// // (m1.qryStart <= _protectOverflow( m2.qryEnd, d)) &&
// // (m1.subjStart >= _protectUnderflow(m2.subjStart,d)) &&
// // (m1.subjStart <= _protectOverflow( m2.subjEnd, d))
// // ) || // OR match endings overlap
// // ((m1.qryEnd >= _protectUnderflow(m2.qryStart, d)) &&
// // (m1.qryEnd <= _protectOverflow( m2.qryEnd, d)) &&
// // (m1.subjEnd >= _protectUnderflow(m2.subjStart,d)) &&
// // (m1.subjEnd <= _protectOverflow( m2.subjEnd, d))
// // )
// // )
// // return true;
//
// //DEBUG DEBUG DEBUG TODO TODO TODO WHEN ALIGNMENT IS FIXED
// // also add check if diffference of overlaps is <= maximum number of gaps
// if ((intervalOverlap(m1.qryStart, m1.qryEnd, m2.qryStart, m2.qryEnd) > -d) &&
// (intervalOverlap(m1.subjStart, m1.subjEnd, m2.subjStart, m2.subjEnd) > -d) &&
// ((m1.qryStart < m2.qryStart ) == (m1.subjStart < m2.subjStart))) // same order
// return true;
//
// return false;
// }
// inline bool contains(Match const & m1, Match const & m2)
// {
// // if (m1.qryId != m2.qryId)
// // return false;
// SEQAN_ASSERT_EQ(m1.qryId, m2.qryId);
// if (m1.qryStart != m2.qryStart)
// return false;
//
// if (m1.qryStart > m2.qryStart)
// return false;
// if (m1.subjStart > m2.subjStart)
// return false;
// if (m1.qryEnd < m2.qryEnd)
// return false;
// if (m1.subjEnd < m2.subjEnd)
// return false;
// return true;
// }
//
// inline void
// mergeUnto(Match & m1, Match const & m2)
// {
// SEQAN_ASSERT_EQ(m1.qryId, m2.qryId);
// SEQAN_ASSERT_EQ(m1.subjId, m2.subjId);
// m1.qryStart = std::min(m1.qryStart, m2.qryStart);
// m1.qryEnd = std::max(m1.qryEnd, m2.qryEnd);
// m1.subjStart = std::min(m1.subjStart,m2.subjStart);
// m1.subjEnd = std::max(m1.subjEnd, m2.subjEnd);
// }
// inline void
// _printMatch(Match const & m)
// {
// std::cout << "MATCH Query " << m.qryId
// << "(" << m.qryStart << ", " << m.qryEnd
// << ") on Subject "<< m.subjId
// << "(" << m.subjStart << ", " << m.subjEnd
// << ")" << std::endl << std::flush;
// }
#endif // header guard
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