SCORE GlobalAlignSS(const Seq &seqA, const Seq &seqB, PWPath &Path)
{
const unsigned uLengthA = seqA.Length();
const unsigned uLengthB = seqB.Length();
const unsigned uPrefixCountA = uLengthA + 1;
const unsigned uPrefixCountB = uLengthB + 1;
AllocDPMem(uLengthA, uLengthB);
SCORE *MPrev = DPM.MPrev;
SCORE *MCurr = DPM.MCurr;
SCORE *MWork = DPM.MWork;
SCORE *DPrev = DPM.DPrev;
SCORE *DCurr = DPM.DCurr;
SCORE *DWork = DPM.DWork;
SCORE **MxRowA = DPM.MxRowA;
unsigned *LettersB = DPM.LettersB;
RowFromSeq(seqA, MxRowA);
LettersFromSeq(seqB, LettersB);
unsigned *uDeletePos = DPM.uDeletePos;
int **TraceBack = DPM.TraceBack;
#if DEBUG
for (unsigned i = 0; i < uPrefixCountA; ++i)
memset(TraceBack[i], 0, uPrefixCountB*sizeof(int));
#endif
// Special case for i=0
TraceBack[0][0] = 0;
MPrev[0] = MxRowA[0][LettersB[0]];
// D(0,0) is -infinity (requires I->D).
DPrev[0] = MINUS_INFINITY;
for (unsigned j = 1; j < uLengthB; ++j)
{
unsigned uLetterB = LettersB[j];
// Only way to get M(0, j) looks like this:
// A ----X
// B XXXXX
// 0 j
// So gap-open at j=0, gap-close at j-1.
MPrev[j] = MxRowA[0][uLetterB] + g_scoreGapOpen/2; // term gaps half
TraceBack[0][j] = -(int) j;
// Assume no D->I transitions, then can't be a delete if only
// one letter from A.
DPrev[j] = MINUS_INFINITY;
}
SCORE IPrev_j_1;
for (unsigned i = 1; i < uLengthA; ++i)
{
SCORE *ptrMCurr_j = MCurr;
memset(ptrMCurr_j, 0, uLengthB*sizeof(SCORE));
const SCORE *RowA = MxRowA[i];
const SCORE *ptrRowA = MxRowA[i];
const SCORE *ptrMCurrEnd = ptrMCurr_j + uLengthB;
unsigned *ptrLettersB = LettersB;
for (; ptrMCurr_j != ptrMCurrEnd; ++ptrMCurr_j)
{
*ptrMCurr_j = RowA[*ptrLettersB];
++ptrLettersB;
}
unsigned *ptrDeletePos = uDeletePos;
// Special case for j=0
// Only way to get M(i, 0) looks like this:
// 0 i
// A XXXXX
// B ----X
// So gap-open at i=0, gap-close at i-1.
ptrMCurr_j = MCurr;
assert(ptrMCurr_j == &(MCurr[0]));
*ptrMCurr_j += g_scoreGapOpen/2; // term gaps half
++ptrMCurr_j;
int *ptrTraceBack_ij = TraceBack[i];
*ptrTraceBack_ij++ = (int) i;
SCORE *ptrMPrev_j = MPrev;
SCORE *ptrDPrev = DPrev;
SCORE d = *ptrDPrev;
SCORE DNew = *ptrMPrev_j + g_scoreGapOpen;
if (DNew > d)
{
d = DNew;
*ptrDeletePos = i;
}
SCORE *ptrDCurr = DCurr;
assert(ptrDCurr == &(DCurr[0]));
*ptrDCurr = d;
// Can't have an insert if no letters from B
IPrev_j_1 = MINUS_INFINITY;
unsigned uInsertPos;
for (unsigned j = 1; j < uLengthB; ++j)
{
// Here, MPrev_j is preserved from previous
// iteration so with current i,j is M[i-1][j-1]
SCORE MPrev_j = *ptrMPrev_j;
SCORE INew = MPrev_j + g_scoreGapOpen;
if (INew > IPrev_j_1)
{
IPrev_j_1 = INew;
uInsertPos = j;
}
SCORE scoreMax = MPrev_j;
assert(ptrDPrev == &(DPrev[j-1]));
SCORE scoreD = *ptrDPrev++;
if (scoreD > scoreMax)
{
scoreMax = scoreD;
assert(ptrDeletePos == &(uDeletePos[j-1]));
*ptrTraceBack_ij = (int) i - (int) *ptrDeletePos;
assert(*ptrTraceBack_ij > 0);
}
++ptrDeletePos;
SCORE scoreI = IPrev_j_1;
if (scoreI > scoreMax)
{
scoreMax = scoreI;
*ptrTraceBack_ij = (int) uInsertPos - (int) j;
assert(*ptrTraceBack_ij < 0);
}
*ptrMCurr_j += scoreMax;
assert(ptrMCurr_j == &(MCurr[j]));
++ptrMCurr_j;
MPrev_j = *(++ptrMPrev_j);
assert(ptrDPrev == &(DPrev[j]));
SCORE d = *ptrDPrev;
SCORE DNew = MPrev_j + g_scoreGapOpen;
if (DNew > d)
{
d = DNew;
assert(ptrDeletePos == &uDeletePos[j]);
*ptrDeletePos = i;
}
assert(ptrDCurr + 1 == &(DCurr[j]));
*(++ptrDCurr) = d;
++ptrTraceBack_ij;
}
Rotate(MPrev, MCurr, MWork);
Rotate(DPrev, DCurr, DWork);
}
// Special case for i=uLengthA
SCORE IPrev = MINUS_INFINITY;
unsigned uInsertPos;
for (unsigned j = 1; j < uLengthB; ++j)
{
SCORE INew = MPrev[j-1];
if (INew > IPrev)
{
uInsertPos = j;
IPrev = INew;
}
}
// Special case for i=uLengthA, j=uLengthB
SCORE scoreMax = MPrev[uLengthB-1];
int iTraceBack = 0;
SCORE scoreD = DPrev[uLengthB-1] - g_scoreGapOpen/2; // term gaps half
if (scoreD > scoreMax)
{
scoreMax = scoreD;
iTraceBack = (int) uLengthA - (int) uDeletePos[uLengthB-1];
}
SCORE scoreI = IPrev - g_scoreGapOpen/2;
if (scoreI > scoreMax)
{
scoreMax = scoreI;
iTraceBack = (int) uInsertPos - (int) uLengthB;
}
TraceBack[uLengthA][uLengthB] = iTraceBack;
TraceBackToPath(TraceBack, uLengthA, uLengthB, Path);
return scoreMax;
}
SCORE GlobalAlignSPN(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path)
{
if (ALPHA_DNA != g_Alpha || ALPHA_RNA == g_Alpha)
Quit("GlobalAlignSPN: must be nucleo");
const unsigned uPrefixCountA = uLengthA + 1;
const unsigned uPrefixCountB = uLengthB + 1;
AllocDPMem(uLengthA, uLengthB);
SCORE *GapOpenA = DPM.GapOpenA;
SCORE *GapOpenB = DPM.GapOpenB;
SCORE *GapCloseA = DPM.GapCloseA;
SCORE *GapCloseB = DPM.GapCloseB;
unsigned **SortOrderA = DPM.SortOrderA;
FCOUNT **FreqsA = DPM.FreqsA;
SCORE **ScoreMxB = DPM.ScoreMxB;
SCORE *MPrev = DPM.MPrev;
SCORE *MCurr = DPM.MCurr;
SCORE *MWork = DPM.MWork;
SCORE *DPrev = DPM.DPrev;
SCORE *DCurr = DPM.DCurr;
SCORE *DWork = DPM.DWork;
unsigned *uDeletePos = DPM.uDeletePos;
int **TraceBack = DPM.TraceBack;
for (unsigned i = 0; i < uLengthA; ++i)
{
GapOpenA[i] = PA[i].m_scoreGapOpen;
GapCloseA[i] = PA[i].m_scoreGapClose;
for (unsigned uLetter = 0; uLetter < 4; ++uLetter)
{
SortOrderA[i][uLetter] = PA[i].m_uSortOrder[uLetter];
FreqsA[i][uLetter] = PA[i].m_fcCounts[uLetter];
}
}
for (unsigned j = 0; j < uLengthB; ++j)
{
GapOpenB[j] = PB[j].m_scoreGapOpen;
GapCloseB[j] = PB[j].m_scoreGapClose;
}
for (unsigned uLetter = 0; uLetter < 4; ++uLetter)
{
for (unsigned j = 0; j < uLengthB; ++j)
ScoreMxB[uLetter][j] = PB[j].m_AAScores[uLetter];
}
for (unsigned i = 0; i < uPrefixCountA; ++i)
memset(TraceBack[i], 0, uPrefixCountB*sizeof(int));
// Special case for i=0
unsigned **ptrSortOrderA = SortOrderA;
FCOUNT **ptrFreqsA = FreqsA;
assert(ptrSortOrderA == &(SortOrderA[0]));
assert(ptrFreqsA == &(FreqsA[0]));
TraceBack[0][0] = 0;
SCORE scoreSum = 0;
unsigned *ptrSortOrderAi = SortOrderA[0];
const unsigned *ptrSortOrderAEnd = ptrSortOrderAi + 4;
FCOUNT *ptrFreqsAi = FreqsA[0];
for (; ptrSortOrderAi != ptrSortOrderAEnd; ++ptrSortOrderAi)
{
const unsigned uLetter = *ptrSortOrderAi;
const FCOUNT fcLetter = ptrFreqsAi[uLetter];
if (0 == fcLetter)
break;
scoreSum += fcLetter*ScoreMxB[uLetter][0];
}
MPrev[0] = scoreSum - g_scoreCenter;
// D(0,0) is -infinity (requires I->D).
DPrev[0] = MINUS_INFINITY;
for (unsigned j = 1; j < uLengthB; ++j)
{
// Only way to get M(0, j) looks like this:
// A ----X
// B XXXXX
// 0 j
// So gap-open at j=0, gap-close at j-1.
SCORE scoreSum = 0;
unsigned *ptrSortOrderAi = SortOrderA[0];
const unsigned *ptrSortOrderAEnd = ptrSortOrderAi + 4;
FCOUNT *ptrFreqsAi = FreqsA[0];
for (; ptrSortOrderAi != ptrSortOrderAEnd; ++ptrSortOrderAi)
{
const unsigned uLetter = *ptrSortOrderAi;
const FCOUNT fcLetter = ptrFreqsAi[uLetter];
if (0 == fcLetter)
break;
scoreSum += fcLetter*ScoreMxB[uLetter][j];
}
MPrev[j] = scoreSum - g_scoreCenter + GapOpenB[0] + GapCloseB[j-1];
TraceBack[0][j] = -(int) j;
// Assume no D->I transitions, then can't be a delete if only
// one letter from A.
DPrev[j] = MINUS_INFINITY;
}
SCORE IPrev_j_1;
for (unsigned i = 1; i < uLengthA; ++i)
{
++ptrSortOrderA;
++ptrFreqsA;
assert(ptrSortOrderA == &(SortOrderA[i]));
assert(ptrFreqsA == &(FreqsA[i]));
SCORE *ptrMCurr_j = MCurr;
memset(ptrMCurr_j, 0, uLengthB*sizeof(SCORE));
const FCOUNT *FreqsAi = *ptrFreqsA;
const unsigned *SortOrderAi = *ptrSortOrderA;
const unsigned *ptrSortOrderAiEnd = SortOrderAi + 4;
const SCORE *ptrMCurrMax = MCurr + uLengthB;
for (const unsigned *ptrSortOrderAi = SortOrderAi;
ptrSortOrderAi != ptrSortOrderAiEnd;
++ptrSortOrderAi)
{
const unsigned uLetter = *ptrSortOrderAi;
SCORE *NSBR_Letter = ScoreMxB[uLetter];
const FCOUNT fcLetter = FreqsAi[uLetter];
if (0 == fcLetter)
break;
SCORE *ptrNSBR = NSBR_Letter;
for (SCORE *ptrMCurr = MCurr; ptrMCurr != ptrMCurrMax; ++ptrMCurr)
*ptrMCurr += fcLetter*(*ptrNSBR++);
}
for (unsigned j = 0; j < uLengthB; ++j)
MCurr[j] -= g_scoreCenter;
ptrMCurr_j = MCurr;
unsigned *ptrDeletePos = uDeletePos;
// Special case for j=0
// Only way to get M(i, 0) looks like this:
// 0 i
// A XXXXX
// B ----X
// So gap-open at i=0, gap-close at i-1.
assert(ptrMCurr_j == &(MCurr[0]));
*ptrMCurr_j += GapOpenA[0] + GapCloseA[i-1];
++ptrMCurr_j;
int *ptrTraceBack_ij = TraceBack[i];
*ptrTraceBack_ij++ = (int) i;
SCORE *ptrMPrev_j = MPrev;
SCORE *ptrDPrev = DPrev;
SCORE d = *ptrDPrev;
SCORE DNew = *ptrMPrev_j + GapOpenA[i];
if (DNew > d)
{
d = DNew;
*ptrDeletePos = i;
}
SCORE *ptrDCurr = DCurr;
assert(ptrDCurr == &(DCurr[0]));
*ptrDCurr = d;
// Can't have an insert if no letters from B
IPrev_j_1 = MINUS_INFINITY;
unsigned uInsertPos;
const SCORE scoreGapOpenAi = GapOpenA[i];
const SCORE scoreGapCloseAi_1 = GapCloseA[i-1];
for (unsigned j = 1; j < uLengthB; ++j)
{
// Here, MPrev_j is preserved from previous
// iteration so with current i,j is M[i-1][j-1]
SCORE MPrev_j = *ptrMPrev_j;
SCORE INew = MPrev_j + GapOpenB[j];
if (INew > IPrev_j_1)
{
IPrev_j_1 = INew;
uInsertPos = j;
}
SCORE scoreMax = MPrev_j;
assert(ptrDPrev == &(DPrev[j-1]));
SCORE scoreD = *ptrDPrev++ + scoreGapCloseAi_1;
if (scoreD > scoreMax)
{
scoreMax = scoreD;
assert(ptrDeletePos == &(uDeletePos[j-1]));
*ptrTraceBack_ij = (int) i - (int) *ptrDeletePos;
assert(*ptrTraceBack_ij > 0);
}
++ptrDeletePos;
SCORE scoreI = IPrev_j_1 + GapCloseB[j-1];
if (scoreI > scoreMax)
{
scoreMax = scoreI;
*ptrTraceBack_ij = (int) uInsertPos - (int) j;
assert(*ptrTraceBack_ij < 0);
}
assert(ptrSortOrderA == &(SortOrderA[i]));
assert(ptrFreqsA == &(FreqsA[i]));
*ptrMCurr_j += scoreMax;
assert(ptrMCurr_j == &(MCurr[j]));
++ptrMCurr_j;
MPrev_j = *(++ptrMPrev_j);
assert(ptrDPrev == &(DPrev[j]));
SCORE d = *ptrDPrev;
SCORE DNew = MPrev_j + scoreGapOpenAi;
if (DNew > d)
{
d = DNew;
assert(ptrDeletePos == &uDeletePos[j]);
*ptrDeletePos = i;
}
assert(ptrDCurr + 1 == &(DCurr[j]));
*(++ptrDCurr) = d;
++ptrTraceBack_ij;
}
Rotate(MPrev, MCurr, MWork);
Rotate(DPrev, DCurr, DWork);
}
// Special case for i=uLengthA
SCORE IPrev = MINUS_INFINITY;
unsigned uInsertPos;
for (unsigned j = 1; j < uLengthB; ++j)
{
SCORE INew = MPrev[j-1] + GapOpenB[j];
if (INew > IPrev)
{
uInsertPos = j;
IPrev = INew;
}
}
// Special case for i=uLengthA, j=uLengthB
SCORE scoreMax = MPrev[uLengthB-1];
int iTraceBack = 0;
SCORE scoreD = DPrev[uLengthB-1] + GapCloseA[uLengthA-1];
if (scoreD > scoreMax)
{
scoreMax = scoreD;
iTraceBack = (int) uLengthA - (int) uDeletePos[uLengthB-1];
}
SCORE scoreI = IPrev + GapCloseB[uLengthB-1];
if (scoreI > scoreMax)
{
scoreMax = scoreI;
iTraceBack = (int) uInsertPos - (int) uLengthB;
}
TraceBack[uLengthA][uLengthB] = iTraceBack;
TraceBackToPath(TraceBack, uLengthA, uLengthB, Path);
return scoreMax;
}