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375 lines (353 loc) · 14.9 KB
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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#ifndef _NUC_PROT_ALIGN_
#define _NUC_PROT_ALIGN_
#include "genetic_code.hpp"
#include "glb_align.hpp"
using namespace std;
namespace DeBruijn {
class CCigar_NAtoAA : public CCigarBase {
public:
CCigar_NAtoAA(int qto, int sto) : CCigarBase(qto, 3*sto+2) {}
TRange SubjectRange() const { return TRange(m_sfrom/3, (m_sto+1)/3-1); }
TCharAlign ToAlign(const char* query, const char* subject) const {
TCharAlign align;
query += m_qfrom;
subject += m_sfrom/3;
for(auto& element : m_elements) {
if(element.m_type == 'M') {
align.first.insert(align.first.end(), query, query+element.m_len);
query += element.m_len;
for(int l = 0; l < element.m_len/3; ++l)
align.second.insert(align.second.end(), 3, *subject++);
if(element.m_len%3 != 0)
align.second.insert(align.second.end(), element.m_len%3, *subject);
} else if(element.m_type == 'D') {
align.first.insert(align.first.end(), element.m_len, '-');
if(element.m_len%3 != 0)
align.second.insert(align.second.end(), element.m_len%3, *subject++);
for(int l = 0; l < element.m_len/3; ++l)
align.second.insert(align.second.end(), 3, *subject++);
} else {
align.first.insert(align.first.end(), query, query+element.m_len);
query += element.m_len;
align.second.insert(align.second.end(), element.m_len, '-');
}
}
return align;
}
int Score(const char* query, const char* subject, int gopen, int gapextend, int fsopen, const char delta[256][256], const GeneticCode& gcode) const {
int score = 0;
const char* pstart = nullptr;
if(m_sfrom == 0 && *subject == 'M')
pstart = subject;
query += m_qfrom;
subject += m_sfrom/3;
for(auto& element : m_elements) {
if(element.m_type == 'M') {
for(int l = 0; l < element.m_len/3; ++l) { // only whole codons
string codon(query, query+3);
if(subject == pstart && gcode.IsStart(codon))
score += delta[(int)'M'][(int)'M'];
else
score += delta[(int)gcode.AA(codon)][(int)*subject];
query += 3;
++subject;
}
} else if(element.m_type == 'D') {
int gap = element.m_len/3;
subject += gap;
int opn = gopen;
if(element.m_len%3 > 0) {
++gap;
++subject;
query += 3-element.m_len%3;
opn = fsopen;
}
score -= opn+gapextend*gap;
} else {
int gap = element.m_len/3;
query += element.m_len;
int opn = gopen;
if(element.m_len%3 > 0) {
++gap;
opn = fsopen;
}
score -= opn+gapextend*gap;
}
}
return score;
}
void PrintAlign(const char* query, const char* subject, const char delta[256][256], const GeneticCode& gcode, ostream& os) const {
bool from_prot_start = (m_sfrom == 0 && *subject == 'M');
TCharAlign align = ToAlign(query, subject);
os << align.first << "\n";
for(unsigned p = 0; p < align.first.size(); p += 3) {
for( ; align.second[p] == '-'; ++p)
os << " ";
string codon = align.first.substr(p, 3);
if(codon.find('-') == string::npos) {
char aa = gcode.AA(codon);
if(aa == align.second[p] || (from_prot_start && p == 0 && gcode.IsStart(codon)))
os << "|||";
else if(delta[(int)aa][(int)align.second[p]] > 0)
os << "+++";
else
os << " ";
} else {
os << " ";
}
}
os << "\n" << align.second << "\n";
}
};
struct SRawMemoryNAtoAA {
SRawMemoryNAtoAA(size_t na, size_t nb) {
for(auto& item : s)
item = new CScore[nb+1]; // constructor called
for(auto& item : gapb)
item = new CScore[nb+1];
for(auto& item : fsb1)
item = new CScore[nb+1];
for(auto& item : fsb2)
item = new CScore[nb+1];
mtrx = new uint16_t[(na+1)*(nb+1)]; //not initialised
for(size_t i = 0; i <= 2*nb; ++i) //two first raws
mtrx[i] = CCigar_NAtoAA::Zero;
}
~SRawMemoryNAtoAA() {
for(auto& item : s)
delete[] item;
for(auto& item : gapb)
delete[] item;
for(auto& item : fsb1)
delete[] item;
for(auto& item : fsb2)
delete[] item;
delete[] mtrx;
}
void Rotate() {
rotate(s.begin(), s.end()-1, s.end());
rotate(gapb.begin(), gapb.end()-1, gapb.end());
rotate(fsb1.begin(), fsb1.end()-1, fsb1.end());
rotate(fsb2.begin(), fsb2.end()-1, fsb2.end());
}
array<CScore*,4> s; // best scores in 4 last raws
array<CScore*,4> gapb; // best gaps (whole codons) in b (insertions in a)
array<CScore*,4> fsb1; // best frameshifts in b (3*n+1 insertions in a)
array<CScore*,4> fsb2; // best frameshifts in b (3*n+2 insertions in a)
uint16_t* mtrx; // backtracking info (Astart/Bstart gap start, Agap/Bgap best score has gap and should be backtracked to Asrt/Bsart; Zero stop bactracking)
};
CCigar_NAtoAA BackTrackNAtoAA(int ia, int ib, uint16_t* m, int nb) {
CCigar_NAtoAA track(ia, ib);
while((ia >= 0 || ib >= 0) && !(*m&CCigar_NAtoAA::Zero)) {
if(*m&CCigar_NAtoAA::Agap) {
int len = 3;
while(!(*m&CCigar_NAtoAA::Astart)) {
len += 3;
--m;
--ib;
}
--m;
--ib;
track.PushFront(CCigar::SElement(len,'D'));
} else if(*m&CCigar_NAtoAA::AgapFS1) {
int len = 1;
while(!(*(m-nb-1)&CCigar_NAtoAA::AstartFS1)) {
len += 3;
--m;
--ib;
}
ia -= 2;
m -= 2*(nb+1)+1; // shift for 2 extra a bases and 1 b base
--ib;
track.PushFront(CCigar::SElement(len,'D'));
track.PushFront(CCigar::SElement(2,'M')); // 2 extra a bases added to left diagonal
} else if(*m&CCigar_NAtoAA::AgapFS2) {
int len = 2;
while(!(*m&CCigar_NAtoAA::AstartFS2)) {
len += 3;
--m;
--ib;
}
--ia;
m -= nb+2; // shift for 1 extra a base and 1 b base
--ib;
track.PushFront(CCigar::SElement(len,'D'));
track.PushFront(CCigar::SElement(1,'M')); // 1 extra a base added to left diagonal
} else if(*m&CCigar_NAtoAA::Bgap) {
int len = 3;
while(!(*m&CCigar_NAtoAA::Bstart)) {
len += 3;
m -= 3*(nb+1);
}
m -= 3*(nb+1);
ia -= len;
track.PushFront(CCigar::SElement(len,'I'));
} else if(*m&CCigar_NAtoAA::BgapFS1) {
int len =1;
while(!(*m&CCigar_NAtoAA::BstartFS1)) {
len += 3;
m -= 3*(nb+1);
}
m -= nb+1;
ia -= len;
track.PushFront(CCigar::SElement(len,'I'));
} else if(*m&CCigar_NAtoAA::BgapFS2) {
int len =2;
while(!(*(m-nb-1)&CCigar_NAtoAA::BstartFS2)) {
len += 3;
m -= 3*(nb+1);
}
m -= 2*(nb+1);
ia -= len;
track.PushFront(CCigar::SElement(len,'I'));
} else {
ia -= 3;
--ib;
m -= 3*(nb+1)+1; //shift for 3 a bases and 1 b base
track.PushFront(CCigar::SElement(3,'M'));
}
}
return track;
}
CCigar_NAtoAA LclAlignNAtoAA(const char* a, int na, const char* b, int nb, int rho, int sigma, int rhofs, const char delta[256][256], const GeneticCode& gcode) {
// rho - new gap penalty (one base gap rho+sigma)
// sigma - extension penalty
// rhofs - new frmeshift penalty (one base gap rho+sigma)
SRawMemoryNAtoAA memory(na, nb);
CScore*& s = memory.s[0]; // best scores in current a-raw
CScore*& sm1 = memory.s[1]; // best scores in -1 a-raw
CScore*& sm2 = memory.s[2]; // best scores in -2 a-raw
CScore*& sm3 = memory.s[3]; // best scores in -3 a-raw
CScore*& gapb = memory.gapb[0]; // best score with b-gap (3*n insertion in a) in current a-raw
CScore*& gapbm3 = memory.gapb[3]; // best score with b-gap (3*n insertion in a) in -3 a-raw
CScore*& fsb1 = memory.fsb1[0]; // best score with b-frameshift (3*n+1 insertion in a) in current a-raw
CScore*& fsb1m3 = memory.fsb1[3]; // best score with b-frameshift (3*n+1 insertion in a) in -3 a-raw
CScore*& fsb2 = memory.fsb2[0]; // best score with b-frameshift (3*n+2 insertion in a) in current a-raw
CScore*& fsb2m3 = memory.fsb2[3]; // best score with b-frameshift (3*n+2 insertion in a) in -3 a-raw
uint16_t* mtrx = memory.mtrx; // backtracking info (Astart/Bstart gap start, Agap/Bgap best score has gap and should be backtracked to Asrt/Bsart; Zero stop bactracking)
CScore rsa(-rho-sigma, 0); // new gapa
CScore rsb(-rho-sigma, 1); // new gapb
CScore rsafs(-rhofs-sigma, 0); // new a-frameshift
CScore rsbfs(-rhofs-sigma, 1); // new b-frameshift
CScore max_score;
uint16_t* max_ptr = mtrx;
uint16_t* m = mtrx+nb+2*(nb+1); // shift to 3rd raw
for(int i = 2; i < na; ++i) {
*(++m) = CCigar_NAtoAA::Zero;
string codon(a+i-2, a+i+1);
const char* matrix = delta[(int)gcode.AA(codon)];
CScore gapa; // 3*n deletion from a
CScore fsa1; // 3*n+1 deletion from a
CScore fsa2; // 3*n+2 deletion from a
for(int j = 0; j < nb; ) {
// b[j] current aa
// any_score[j] score for previous aa
// any_score[j+1] score for current aa
*(++m) = 0;
CScore ss = sm3[j]+CScore(matrix[(int)b[j]], 1); // diagonal extension
if(j == 0 && b[j] == 'M' && gcode.IsStart(codon)) // possible alt start
ss = sm3[j]+CScore(delta[(int)'M'][(int)'M'], 1);
gapa += CScore(-sigma, 0); // gapa extension (3*n deletion)
if(s[j]+rsa > gapa) {
gapa = s[j]+rsa; // new gapa
*m |= CCigar_NAtoAA::Astart; // the end of last aligned NA codon, first inserted AA
}
fsa1 += CScore(-sigma, 0); // fsa extension (3*n+1 deletion)
if(sm2[j]+rsafs > fsa1) {
fsa1 = sm2[j]+rsafs;
*(m-nb-1) |= CCigar_NAtoAA::AstartFS2; // first not aligned NA base, first inserted AA
}
fsa2 += CScore(-sigma, 0); // fsa extension (3*n+2 deletion)
if(sm1[j]+rsafs > fsa2) {
fsa2 = sm1[j]+rsafs;
*m |= CCigar_NAtoAA::AstartFS1; // first not aligned NA base, first inserted AA
}
CScore& gapbj = gapb[++j]; // j increased here
gapbj = gapbm3[j]+CScore(-sigma, 1); // gapb extension
if(sm3[j]+rsb > gapbj) {
gapbj = sm3[j]+rsb; // new gapb
*m |= CCigar_NAtoAA::Bstart; // the end of first insertion codon in NA, last aligned AA
}
CScore& fsb1j = fsb1[j];
fsb1j = fsb1m3[j]+CScore(-sigma, 1); // fsb1 extension
if(sm1[j]+rsbfs > fsb1j) {
fsb1j = sm1[j]+rsbfs;
*m |= CCigar_NAtoAA::BstartFS1; // first not aligned NA base, last aligned AA
}
CScore& fsb2j = fsb2[j];
fsb2j = fsb2m3[j]+CScore(-sigma, 1); // fsb2 extension
if(sm2[j]+rsbfs > fsb2j) {
fsb2j = sm2[j]+rsbfs;
*(m-nb-1) |= CCigar_NAtoAA::BstartFS2; // first not aligned NA base, last aligned AA
}
int type = 0;
CScore score = ss;
if(gapa > score) {
score = gapa;
type = CCigar_NAtoAA::Agap;
}
if(fsa1 > score) {
score = fsa1;
type = CCigar_NAtoAA::AgapFS1;
}
if(fsa2 > score) {
score = fsa2;
type = CCigar_NAtoAA::AgapFS2;
}
if(gapbj > score) {
score = gapbj;
type = CCigar_NAtoAA::Bgap;
}
if(fsb1j > score) {
score = fsb1j;
type = CCigar_NAtoAA::BgapFS1;
}
if(fsb2j > score) {
score = fsb2j;
type = CCigar_NAtoAA::BgapFS2;
}
s[j] = score;
*m |= type;
if(type == 0 && score > max_score) {
max_score = score;
max_ptr = m;
}
if(s[j].Score() <= 0) {
s[j] = CScore();
*m |= CCigar_NAtoAA::Zero;
}
}
memory.Rotate();
}
int ia = (max_ptr-mtrx)/(nb+1)-1;
int ib = (max_ptr-mtrx)%(nb+1)-1;
m = max_ptr;
return BackTrackNAtoAA(ia, ib, m, nb);
}
} // namespace
#endif // _NUC_PROT_ALIGN_