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/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 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.
*
* Bowtie 2 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 Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef ALIGNER_SW_NUC_H_
#define ALIGNER_SW_NUC_H_
#include <stdint.h>
#include "aligner_sw_common.h"
#include "aligner_result.h"
/**
* Encapsulates a backtrace stack frame. Includes enough information that we
* can "pop" back up to this frame and choose to make a different backtracking
* decision. The information included is:
*
* 1. The mask at the decision point. When we first move through the mask and
* when we backtrack to it, we're careful to mask out the bit corresponding
* to the path we're taking. When we move through it after removing the
* last bit from the mask, we're careful to pop it from the stack.
* 2. The sizes of the edit lists. When we backtrack, we resize the lists back
* down to these sizes to get rid of any edits introduced since the branch
* point.
*/
struct DpNucFrame {
/**
* Initialize a new DpNucFrame stack frame.
*/
void init(
size_t nedsz_,
size_t aedsz_,
size_t celsz_,
size_t row_,
size_t col_,
size_t gaps_,
size_t readGaps_,
size_t refGaps_,
AlnScore score_,
int ct_)
{
nedsz = nedsz_;
aedsz = aedsz_;
celsz = celsz_;
row = row_;
col = col_;
gaps = gaps_;
readGaps = readGaps_;
refGaps = refGaps_;
score = score_;
ct = ct_;
}
size_t nedsz; // size of the nucleotide edit list at branch (before
// adding the branch edit)
size_t aedsz; // size of ambiguous nucleotide edit list at branch
size_t celsz; // size of cell-traversed list at branch
size_t row; // row of cell where branch occurred
size_t col; // column of cell where branch occurred
size_t gaps; // number of gaps before branch occurred
size_t readGaps; // number of read gaps before branch occurred
size_t refGaps; // number of ref gaps before branch occurred
AlnScore score; // score where branch occurred
int ct; // table type (oall, rdgap or rfgap)
};
enum {
BT_CAND_FATE_SUCCEEDED = 1,
BT_CAND_FATE_FAILED,
BT_CAND_FATE_FILT_START, // skipped b/c starting cell already explored
BT_CAND_FATE_FILT_DOMINATED, // skipped b/c it was dominated
BT_CAND_FATE_FILT_SCORE // skipped b/c score not interesting anymore
};
/**
* Encapsulates a cell that we might want to backtrace from.
*/
struct DpBtCandidate {
DpBtCandidate() { reset(); }
DpBtCandidate(size_t row_, size_t col_, TAlScore score_) {
init(row_, col_, score_);
}
void reset() { init(0, 0, 0); }
void init(size_t row_, size_t col_, TAlScore score_) {
row = row_;
col = col_;
score = score_;
// 0 = invalid; this should be set later according to what happens
// before / during the backtrace
fate = 0;
}
/**
* Return true iff this candidate is (heuristically) dominated by the given
* candidate. We say that candidate A dominates candidate B if (a) B is
* somewhere in the N x N square that extends up and to the left of A,
* where N is an arbitrary number like 20, and (b) B's score is <= than
* A's.
*/
inline bool dominatedBy(const DpBtCandidate& o) {
const size_t SQ = 40;
size_t rowhi = row;
size_t rowlo = o.row;
if(rowhi < rowlo) swap(rowhi, rowlo);
size_t colhi = col;
size_t collo = o.col;
if(colhi < collo) swap(colhi, collo);
return (colhi - collo) <= SQ &&
(rowhi - rowlo) <= SQ;
}
/**
* Return true if this candidate is "greater than" (should be considered
* later than) the given candidate.
*/
bool operator>(const DpBtCandidate& o) const {
if(score < o.score) return true;
if(score > o.score) return false;
if(row < o.row ) return true;
if(row > o.row ) return false;
if(col < o.col ) return true;
if(col > o.col ) return false;
return false;
}
/**
* Return true if this candidate is "less than" (should be considered
* sooner than) the given candidate.
*/
bool operator<(const DpBtCandidate& o) const {
if(score > o.score) return true;
if(score < o.score) return false;
if(row > o.row ) return true;
if(row < o.row ) return false;
if(col > o.col ) return true;
if(col < o.col ) return false;
return false;
}
/**
* Return true if this candidate equals the given candidate.
*/
bool operator==(const DpBtCandidate& o) const {
return row == o.row &&
col == o.col &&
score == o.score;
}
bool operator>=(const DpBtCandidate& o) const { return !((*this) < o); }
bool operator<=(const DpBtCandidate& o) const { return !((*this) > o); }
#ifndef NDEBUG
/**
* Check internal consistency.
*/
bool repOk() const {
assert(VALID_SCORE(score));
return true;
}
#endif
size_t row; // cell row
size_t col; // cell column w/r/t LHS of rectangle
TAlScore score; // score fo alignment
int fate; // flag indicating whether we succeeded, failed, skipped
};
template <typename T>
class NBest {
public:
NBest<T>() { nelt_ = nbest_ = n_ = 0; }
bool inited() const { return nelt_ > 0; }
void init(size_t nelt, size_t nbest) {
nelt_ = nelt;
nbest_ = nbest;
elts_.resize(nelt * nbest);
ncur_.resize(nelt);
ncur_.fill(0);
n_ = 0;
}
/**
* Add a new result to bin 'elt'. Where it gets prioritized in the list of
* results in that bin depends on the result of operator>.
*/
bool add(size_t elt, const T& o) {
assert_lt(elt, nelt_);
const size_t ncur = ncur_[elt];
assert_leq(ncur, nbest_);
n_++;
for(size_t i = 0; i < nbest_ && i <= ncur; i++) {
if(o > elts_[nbest_ * elt + i] || i >= ncur) {
// Insert it here
// Move everyone from here on down by one slot
for(int j = (int)ncur; j > (int)i; j--) {
if(j < (int)nbest_) {
elts_[nbest_ * elt + j] = elts_[nbest_ * elt + j - 1];
}
}
elts_[nbest_ * elt + i] = o;
if(ncur < nbest_) {
ncur_[elt]++;
}
return true;
}
}
return false;
}
/**
* Return true iff there are no solutions.
*/
bool empty() const {
return n_ == 0;
}
/**
* Dump all the items in our payload into the given EList.
*/
template<typename TList>
void dump(TList& l) const {
if(empty()) return;
for(size_t i = 0; i < nelt_; i++) {
assert_leq(ncur_[i], nbest_);
for(size_t j = 0; j < ncur_[i]; j++) {
l.push_back(elts_[i * nbest_ + j]);
}
}
}
protected:
size_t nelt_;
size_t nbest_;
EList<T> elts_;
EList<size_t> ncur_;
size_t n_; // total # results added
};
#endif /*def ALIGNER_SW_NUC_H_*/
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