19 unsigned **SortOrderA;
\r
20 unsigned *uDeletePos;
\r
25 static struct DP_MEMORY DPM;
\r
29 const unsigned uOldLength = DPM.uLength;
\r
30 if (0 == uOldLength)
\r
33 for (unsigned i = 0; i < uOldLength; ++i)
\r
35 delete[] DPM.TraceBack[i];
\r
36 delete[] DPM.FreqsA[i];
\r
37 delete[] DPM.SortOrderA[i];
\r
39 for (unsigned n = 0; n < 4; ++n)
\r
40 delete[] DPM.ScoreMxB[n];
\r
48 delete[] DPM.uDeletePos;
\r
49 delete[] DPM.GapOpenA;
\r
50 delete[] DPM.GapOpenB;
\r
51 delete[] DPM.GapCloseA;
\r
52 delete[] DPM.GapCloseB;
\r
53 delete[] DPM.SortOrderA;
\r
54 delete[] DPM.FreqsA;
\r
55 delete[] DPM.ScoreMxB;
\r
56 delete[] DPM.TraceBack;
\r
59 static void AllocDPMem(unsigned uLengthA, unsigned uLengthB)
\r
61 // Max prefix length
\r
62 unsigned uLength = (uLengthA > uLengthB ? uLengthA : uLengthB) + 1;
\r
63 if (uLength < DPM.uLength)
\r
66 // Add 256 to allow for future expansion and
\r
67 // round up to next multiple of 32.
\r
69 uLength += 32 - uLength%32;
\r
71 const unsigned uOldLength = DPM.uLength;
\r
74 for (unsigned i = 0; i < uOldLength; ++i)
\r
76 delete[] DPM.TraceBack[i];
\r
77 delete[] DPM.FreqsA[i];
\r
78 delete[] DPM.SortOrderA[i];
\r
80 for (unsigned n = 0; n < 4; ++n)
\r
81 delete[] DPM.ScoreMxB[n];
\r
89 delete[] DPM.uDeletePos;
\r
90 delete[] DPM.GapOpenA;
\r
91 delete[] DPM.GapOpenB;
\r
92 delete[] DPM.GapCloseA;
\r
93 delete[] DPM.GapCloseB;
\r
94 delete[] DPM.SortOrderA;
\r
95 delete[] DPM.FreqsA;
\r
96 delete[] DPM.ScoreMxB;
\r
97 delete[] DPM.TraceBack;
\r
100 DPM.uLength = uLength;
\r
102 DPM.GapOpenA = new SCORE[uLength];
\r
103 DPM.GapOpenB = new SCORE[uLength];
\r
104 DPM.GapCloseA = new SCORE[uLength];
\r
105 DPM.GapCloseB = new SCORE[uLength];
\r
107 DPM.SortOrderA = new unsigned*[uLength];
\r
108 DPM.FreqsA = new FCOUNT*[uLength];
\r
109 DPM.ScoreMxB = new SCORE*[4];
\r
110 DPM.MPrev = new SCORE[uLength];
\r
111 DPM.MCurr = new SCORE[uLength];
\r
112 DPM.MWork = new SCORE[uLength];
\r
114 DPM.DPrev = new SCORE[uLength];
\r
115 DPM.DCurr = new SCORE[uLength];
\r
116 DPM.DWork = new SCORE[uLength];
\r
117 DPM.uDeletePos = new unsigned[uLength];
\r
119 DPM.TraceBack = new int*[uLength];
\r
121 for (unsigned uLetter = 0; uLetter < 4; ++uLetter)
\r
122 DPM.ScoreMxB[uLetter] = new SCORE[uLength];
\r
124 for (unsigned i = 0; i < uLength; ++i)
\r
126 DPM.SortOrderA[i] = new unsigned[4];
\r
127 DPM.FreqsA[i] = new FCOUNT[4];
\r
128 DPM.TraceBack[i] = new int[uLength];
\r
132 SCORE GlobalAlignSPN(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
\r
133 unsigned uLengthB, PWPath &Path)
\r
135 if (ALPHA_DNA != g_Alpha || ALPHA_RNA == g_Alpha)
\r
136 Quit("GlobalAlignSPN: must be nucleo");
\r
138 const unsigned uPrefixCountA = uLengthA + 1;
\r
139 const unsigned uPrefixCountB = uLengthB + 1;
\r
141 AllocDPMem(uLengthA, uLengthB);
\r
143 SCORE *GapOpenA = DPM.GapOpenA;
\r
144 SCORE *GapOpenB = DPM.GapOpenB;
\r
145 SCORE *GapCloseA = DPM.GapCloseA;
\r
146 SCORE *GapCloseB = DPM.GapCloseB;
\r
148 unsigned **SortOrderA = DPM.SortOrderA;
\r
149 FCOUNT **FreqsA = DPM.FreqsA;
\r
150 SCORE **ScoreMxB = DPM.ScoreMxB;
\r
151 SCORE *MPrev = DPM.MPrev;
\r
152 SCORE *MCurr = DPM.MCurr;
\r
153 SCORE *MWork = DPM.MWork;
\r
155 SCORE *DPrev = DPM.DPrev;
\r
156 SCORE *DCurr = DPM.DCurr;
\r
157 SCORE *DWork = DPM.DWork;
\r
158 unsigned *uDeletePos = DPM.uDeletePos;
\r
160 int **TraceBack = DPM.TraceBack;
\r
162 for (unsigned i = 0; i < uLengthA; ++i)
\r
164 GapOpenA[i] = PA[i].m_scoreGapOpen;
\r
165 GapCloseA[i] = PA[i].m_scoreGapClose;
\r
167 for (unsigned uLetter = 0; uLetter < 4; ++uLetter)
\r
169 SortOrderA[i][uLetter] = PA[i].m_uSortOrder[uLetter];
\r
170 FreqsA[i][uLetter] = PA[i].m_fcCounts[uLetter];
\r
174 for (unsigned j = 0; j < uLengthB; ++j)
\r
176 GapOpenB[j] = PB[j].m_scoreGapOpen;
\r
177 GapCloseB[j] = PB[j].m_scoreGapClose;
\r
180 for (unsigned uLetter = 0; uLetter < 4; ++uLetter)
\r
182 for (unsigned j = 0; j < uLengthB; ++j)
\r
183 ScoreMxB[uLetter][j] = PB[j].m_AAScores[uLetter];
\r
186 for (unsigned i = 0; i < uPrefixCountA; ++i)
\r
187 memset(TraceBack[i], 0, uPrefixCountB*sizeof(int));
\r
189 // Special case for i=0
\r
190 unsigned **ptrSortOrderA = SortOrderA;
\r
191 FCOUNT **ptrFreqsA = FreqsA;
\r
192 assert(ptrSortOrderA == &(SortOrderA[0]));
\r
193 assert(ptrFreqsA == &(FreqsA[0]));
\r
194 TraceBack[0][0] = 0;
\r
196 SCORE scoreSum = 0;
\r
197 unsigned *ptrSortOrderAi = SortOrderA[0];
\r
198 const unsigned *ptrSortOrderAEnd = ptrSortOrderAi + 4;
\r
199 FCOUNT *ptrFreqsAi = FreqsA[0];
\r
200 for (; ptrSortOrderAi != ptrSortOrderAEnd; ++ptrSortOrderAi)
\r
202 const unsigned uLetter = *ptrSortOrderAi;
\r
203 const FCOUNT fcLetter = ptrFreqsAi[uLetter];
\r
206 scoreSum += fcLetter*ScoreMxB[uLetter][0];
\r
208 MPrev[0] = scoreSum - g_scoreCenter;
\r
210 // D(0,0) is -infinity (requires I->D).
\r
211 DPrev[0] = MINUS_INFINITY;
\r
213 for (unsigned j = 1; j < uLengthB; ++j)
\r
215 // Only way to get M(0, j) looks like this:
\r
219 // So gap-open at j=0, gap-close at j-1.
\r
220 SCORE scoreSum = 0;
\r
221 unsigned *ptrSortOrderAi = SortOrderA[0];
\r
222 const unsigned *ptrSortOrderAEnd = ptrSortOrderAi + 4;
\r
223 FCOUNT *ptrFreqsAi = FreqsA[0];
\r
224 for (; ptrSortOrderAi != ptrSortOrderAEnd; ++ptrSortOrderAi)
\r
226 const unsigned uLetter = *ptrSortOrderAi;
\r
227 const FCOUNT fcLetter = ptrFreqsAi[uLetter];
\r
230 scoreSum += fcLetter*ScoreMxB[uLetter][j];
\r
232 MPrev[j] = scoreSum - g_scoreCenter + GapOpenB[0] + GapCloseB[j-1];
\r
233 TraceBack[0][j] = -(int) j;
\r
235 // Assume no D->I transitions, then can't be a delete if only
\r
236 // one letter from A.
\r
237 DPrev[j] = MINUS_INFINITY;
\r
241 for (unsigned i = 1; i < uLengthA; ++i)
\r
245 assert(ptrSortOrderA == &(SortOrderA[i]));
\r
246 assert(ptrFreqsA == &(FreqsA[i]));
\r
248 SCORE *ptrMCurr_j = MCurr;
\r
249 memset(ptrMCurr_j, 0, uLengthB*sizeof(SCORE));
\r
250 const FCOUNT *FreqsAi = *ptrFreqsA;
\r
252 const unsigned *SortOrderAi = *ptrSortOrderA;
\r
253 const unsigned *ptrSortOrderAiEnd = SortOrderAi + 4;
\r
254 const SCORE *ptrMCurrMax = MCurr + uLengthB;
\r
255 for (const unsigned *ptrSortOrderAi = SortOrderAi;
\r
256 ptrSortOrderAi != ptrSortOrderAiEnd;
\r
259 const unsigned uLetter = *ptrSortOrderAi;
\r
260 SCORE *NSBR_Letter = ScoreMxB[uLetter];
\r
261 const FCOUNT fcLetter = FreqsAi[uLetter];
\r
264 SCORE *ptrNSBR = NSBR_Letter;
\r
265 for (SCORE *ptrMCurr = MCurr; ptrMCurr != ptrMCurrMax; ++ptrMCurr)
\r
266 *ptrMCurr += fcLetter*(*ptrNSBR++);
\r
269 for (unsigned j = 0; j < uLengthB; ++j)
\r
270 MCurr[j] -= g_scoreCenter;
\r
272 ptrMCurr_j = MCurr;
\r
273 unsigned *ptrDeletePos = uDeletePos;
\r
275 // Special case for j=0
\r
276 // Only way to get M(i, 0) looks like this:
\r
280 // So gap-open at i=0, gap-close at i-1.
\r
281 assert(ptrMCurr_j == &(MCurr[0]));
\r
282 *ptrMCurr_j += GapOpenA[0] + GapCloseA[i-1];
\r
286 int *ptrTraceBack_ij = TraceBack[i];
\r
287 *ptrTraceBack_ij++ = (int) i;
\r
289 SCORE *ptrMPrev_j = MPrev;
\r
290 SCORE *ptrDPrev = DPrev;
\r
291 SCORE d = *ptrDPrev;
\r
292 SCORE DNew = *ptrMPrev_j + GapOpenA[i];
\r
299 SCORE *ptrDCurr = DCurr;
\r
301 assert(ptrDCurr == &(DCurr[0]));
\r
304 // Can't have an insert if no letters from B
\r
305 IPrev_j_1 = MINUS_INFINITY;
\r
307 unsigned uInsertPos;
\r
308 const SCORE scoreGapOpenAi = GapOpenA[i];
\r
309 const SCORE scoreGapCloseAi_1 = GapCloseA[i-1];
\r
311 for (unsigned j = 1; j < uLengthB; ++j)
\r
313 // Here, MPrev_j is preserved from previous
\r
314 // iteration so with current i,j is M[i-1][j-1]
\r
315 SCORE MPrev_j = *ptrMPrev_j;
\r
316 SCORE INew = MPrev_j + GapOpenB[j];
\r
317 if (INew > IPrev_j_1)
\r
323 SCORE scoreMax = MPrev_j;
\r
325 assert(ptrDPrev == &(DPrev[j-1]));
\r
326 SCORE scoreD = *ptrDPrev++ + scoreGapCloseAi_1;
\r
327 if (scoreD > scoreMax)
\r
330 assert(ptrDeletePos == &(uDeletePos[j-1]));
\r
331 *ptrTraceBack_ij = (int) i - (int) *ptrDeletePos;
\r
332 assert(*ptrTraceBack_ij > 0);
\r
336 SCORE scoreI = IPrev_j_1 + GapCloseB[j-1];
\r
337 if (scoreI > scoreMax)
\r
340 *ptrTraceBack_ij = (int) uInsertPos - (int) j;
\r
341 assert(*ptrTraceBack_ij < 0);
\r
344 assert(ptrSortOrderA == &(SortOrderA[i]));
\r
345 assert(ptrFreqsA == &(FreqsA[i]));
\r
347 *ptrMCurr_j += scoreMax;
\r
348 assert(ptrMCurr_j == &(MCurr[j]));
\r
351 MPrev_j = *(++ptrMPrev_j);
\r
352 assert(ptrDPrev == &(DPrev[j]));
\r
353 SCORE d = *ptrDPrev;
\r
354 SCORE DNew = MPrev_j + scoreGapOpenAi;
\r
358 assert(ptrDeletePos == &uDeletePos[j]);
\r
361 assert(ptrDCurr + 1 == &(DCurr[j]));
\r
367 Rotate(MPrev, MCurr, MWork);
\r
368 Rotate(DPrev, DCurr, DWork);
\r
371 // Special case for i=uLengthA
\r
372 SCORE IPrev = MINUS_INFINITY;
\r
374 unsigned uInsertPos;
\r
376 for (unsigned j = 1; j < uLengthB; ++j)
\r
378 SCORE INew = MPrev[j-1] + GapOpenB[j];
\r
386 // Special case for i=uLengthA, j=uLengthB
\r
387 SCORE scoreMax = MPrev[uLengthB-1];
\r
388 int iTraceBack = 0;
\r
390 SCORE scoreD = DPrev[uLengthB-1] + GapCloseA[uLengthA-1];
\r
391 if (scoreD > scoreMax)
\r
394 iTraceBack = (int) uLengthA - (int) uDeletePos[uLengthB-1];
\r
397 SCORE scoreI = IPrev + GapCloseB[uLengthB-1];
\r
398 if (scoreI > scoreMax)
\r
401 iTraceBack = (int) uInsertPos - (int) uLengthB;
\r
404 TraceBack[uLengthA][uLengthB] = iTraceBack;
\r
406 TraceBackToPath(TraceBack, uLengthA, uLengthB, Path);
\r