19 unsigned **SortOrderA;
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20 unsigned *uDeletePos;
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25 static struct DP_MEMORY DPM;
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27 static void AllocDPMem(unsigned uLengthA, unsigned uLengthB)
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29 // Max prefix length
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30 unsigned uLength = (uLengthA > uLengthB ? uLengthA : uLengthB) + 1;
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31 if (uLength < DPM.uLength)
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34 // Add 256 to allow for future expansion and
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35 // round up to next multiple of 32.
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37 uLength += 32 - uLength%32;
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39 const unsigned uOldLength = DPM.uLength;
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42 for (unsigned i = 0; i < uOldLength; ++i)
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44 delete[] DPM.TraceBack[i];
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45 delete[] DPM.FreqsA[i];
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46 delete[] DPM.SortOrderA[i];
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48 for (unsigned n = 0; n < 20; ++n)
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49 delete[] DPM.ScoreMxB[n];
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57 delete[] DPM.uDeletePos;
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58 delete[] DPM.GapOpenA;
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59 delete[] DPM.GapOpenB;
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60 delete[] DPM.GapCloseA;
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61 delete[] DPM.GapCloseB;
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62 delete[] DPM.SortOrderA;
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63 delete[] DPM.FreqsA;
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64 delete[] DPM.ScoreMxB;
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65 delete[] DPM.TraceBack;
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68 DPM.uLength = uLength;
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70 DPM.GapOpenA = new SCORE[uLength];
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71 DPM.GapOpenB = new SCORE[uLength];
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72 DPM.GapCloseA = new SCORE[uLength];
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73 DPM.GapCloseB = new SCORE[uLength];
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75 DPM.SortOrderA = new unsigned*[uLength];
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76 DPM.FreqsA = new FCOUNT*[uLength];
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77 DPM.ScoreMxB = new SCORE*[20];
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78 DPM.MPrev = new SCORE[uLength];
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79 DPM.MCurr = new SCORE[uLength];
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80 DPM.MWork = new SCORE[uLength];
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82 DPM.DPrev = new SCORE[uLength];
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83 DPM.DCurr = new SCORE[uLength];
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84 DPM.DWork = new SCORE[uLength];
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85 DPM.uDeletePos = new unsigned[uLength];
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87 DPM.TraceBack = new int*[uLength];
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89 for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
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90 DPM.ScoreMxB[uLetter] = new SCORE[uLength];
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92 for (unsigned i = 0; i < uLength; ++i)
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94 DPM.SortOrderA[i] = new unsigned[20];
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95 DPM.FreqsA[i] = new FCOUNT[20];
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96 DPM.TraceBack[i] = new int[uLength];
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100 SCORE GlobalAlignSP(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
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101 unsigned uLengthB, PWPath &Path)
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103 const unsigned uPrefixCountA = uLengthA + 1;
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104 const unsigned uPrefixCountB = uLengthB + 1;
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106 AllocDPMem(uLengthA, uLengthB);
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108 SCORE *GapOpenA = DPM.GapOpenA;
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109 SCORE *GapOpenB = DPM.GapOpenB;
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110 SCORE *GapCloseA = DPM.GapCloseA;
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111 SCORE *GapCloseB = DPM.GapCloseB;
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113 unsigned **SortOrderA = DPM.SortOrderA;
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114 FCOUNT **FreqsA = DPM.FreqsA;
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115 SCORE **ScoreMxB = DPM.ScoreMxB;
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116 SCORE *MPrev = DPM.MPrev;
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117 SCORE *MCurr = DPM.MCurr;
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118 SCORE *MWork = DPM.MWork;
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120 SCORE *DPrev = DPM.DPrev;
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121 SCORE *DCurr = DPM.DCurr;
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122 SCORE *DWork = DPM.DWork;
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123 unsigned *uDeletePos = DPM.uDeletePos;
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125 int **TraceBack = DPM.TraceBack;
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127 for (unsigned i = 0; i < uLengthA; ++i)
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129 GapOpenA[i] = PA[i].m_scoreGapOpen;
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130 GapCloseA[i] = PA[i].m_scoreGapClose;
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132 for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
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134 SortOrderA[i][uLetter] = PA[i].m_uSortOrder[uLetter];
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135 FreqsA[i][uLetter] = PA[i].m_fcCounts[uLetter];
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139 for (unsigned j = 0; j < uLengthB; ++j)
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141 GapOpenB[j] = PB[j].m_scoreGapOpen;
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142 GapCloseB[j] = PB[j].m_scoreGapClose;
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145 for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
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147 for (unsigned j = 0; j < uLengthB; ++j)
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148 ScoreMxB[uLetter][j] = PB[j].m_AAScores[uLetter];
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151 for (unsigned i = 0; i < uPrefixCountA; ++i)
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152 memset(TraceBack[i], 0, uPrefixCountB*sizeof(int));
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154 // Special case for i=0
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155 unsigned **ptrSortOrderA = SortOrderA;
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156 FCOUNT **ptrFreqsA = FreqsA;
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157 assert(ptrSortOrderA == &(SortOrderA[0]));
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158 assert(ptrFreqsA == &(FreqsA[0]));
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159 TraceBack[0][0] = 0;
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161 SCORE scoreSum = 0;
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162 unsigned *ptrSortOrderAi = SortOrderA[0];
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163 const unsigned *ptrSortOrderAEnd = ptrSortOrderAi + 20;
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164 FCOUNT *ptrFreqsAi = FreqsA[0];
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165 for (; ptrSortOrderAi != ptrSortOrderAEnd; ++ptrSortOrderAi)
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167 const unsigned uLetter = *ptrSortOrderAi;
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168 const FCOUNT fcLetter = ptrFreqsAi[uLetter];
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171 scoreSum += fcLetter*ScoreMxB[uLetter][0];
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173 MPrev[0] = scoreSum - g_scoreCenter;
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175 // D(0,0) is -infinity (requires I->D).
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176 DPrev[0] = MINUS_INFINITY;
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178 for (unsigned j = 1; j < uLengthB; ++j)
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180 // Only way to get M(0, j) looks like this:
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184 // So gap-open at j=0, gap-close at j-1.
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185 SCORE scoreSum = 0;
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186 unsigned *ptrSortOrderAi = SortOrderA[0];
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187 const unsigned *ptrSortOrderAEnd = ptrSortOrderAi + 20;
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188 FCOUNT *ptrFreqsAi = FreqsA[0];
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189 for (; ptrSortOrderAi != ptrSortOrderAEnd; ++ptrSortOrderAi)
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191 const unsigned uLetter = *ptrSortOrderAi;
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192 const FCOUNT fcLetter = ptrFreqsAi[uLetter];
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195 scoreSum += fcLetter*ScoreMxB[uLetter][j];
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197 MPrev[j] = scoreSum - g_scoreCenter + GapOpenB[0] + GapCloseB[j-1];
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198 TraceBack[0][j] = -(int) j;
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200 // Assume no D->I transitions, then can't be a delete if only
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201 // one letter from A.
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202 DPrev[j] = MINUS_INFINITY;
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206 for (unsigned i = 1; i < uLengthA; ++i)
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210 assert(ptrSortOrderA == &(SortOrderA[i]));
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211 assert(ptrFreqsA == &(FreqsA[i]));
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213 SCORE *ptrMCurr_j = MCurr;
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214 memset(ptrMCurr_j, 0, uLengthB*sizeof(SCORE));
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215 const FCOUNT *FreqsAi = *ptrFreqsA;
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217 const unsigned *SortOrderAi = *ptrSortOrderA;
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218 const unsigned *ptrSortOrderAiEnd = SortOrderAi + 20;
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219 const SCORE *ptrMCurrMax = MCurr + uLengthB;
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220 for (const unsigned *ptrSortOrderAi = SortOrderAi;
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221 ptrSortOrderAi != ptrSortOrderAiEnd;
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224 const unsigned uLetter = *ptrSortOrderAi;
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225 SCORE *NSBR_Letter = ScoreMxB[uLetter];
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226 const FCOUNT fcLetter = FreqsAi[uLetter];
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229 SCORE *ptrNSBR = NSBR_Letter;
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230 for (SCORE *ptrMCurr = MCurr; ptrMCurr != ptrMCurrMax; ++ptrMCurr)
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231 *ptrMCurr += fcLetter*(*ptrNSBR++);
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234 for (unsigned j = 0; j < uLengthB; ++j)
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235 MCurr[j] -= g_scoreCenter;
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237 ptrMCurr_j = MCurr;
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238 unsigned *ptrDeletePos = uDeletePos;
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240 // Special case for j=0
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241 // Only way to get M(i, 0) looks like this:
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245 // So gap-open at i=0, gap-close at i-1.
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246 assert(ptrMCurr_j == &(MCurr[0]));
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247 *ptrMCurr_j += GapOpenA[0] + GapCloseA[i-1];
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251 int *ptrTraceBack_ij = TraceBack[i];
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252 *ptrTraceBack_ij++ = (int) i;
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254 SCORE *ptrMPrev_j = MPrev;
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255 SCORE *ptrDPrev = DPrev;
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256 SCORE d = *ptrDPrev;
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257 SCORE DNew = *ptrMPrev_j + GapOpenA[i];
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264 SCORE *ptrDCurr = DCurr;
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266 assert(ptrDCurr == &(DCurr[0]));
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269 // Can't have an insert if no letters from B
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270 IPrev_j_1 = MINUS_INFINITY;
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272 unsigned uInsertPos;
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273 const SCORE scoreGapOpenAi = GapOpenA[i];
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274 const SCORE scoreGapCloseAi_1 = GapCloseA[i-1];
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276 for (unsigned j = 1; j < uLengthB; ++j)
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278 // Here, MPrev_j is preserved from previous
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279 // iteration so with current i,j is M[i-1][j-1]
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280 SCORE MPrev_j = *ptrMPrev_j;
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281 SCORE INew = MPrev_j + GapOpenB[j];
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282 if (INew > IPrev_j_1)
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288 SCORE scoreMax = MPrev_j;
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290 assert(ptrDPrev == &(DPrev[j-1]));
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291 SCORE scoreD = *ptrDPrev++ + scoreGapCloseAi_1;
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292 if (scoreD > scoreMax)
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295 assert(ptrDeletePos == &(uDeletePos[j-1]));
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296 *ptrTraceBack_ij = (int) i - (int) *ptrDeletePos;
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297 assert(*ptrTraceBack_ij > 0);
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301 SCORE scoreI = IPrev_j_1 + GapCloseB[j-1];
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302 if (scoreI > scoreMax)
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305 *ptrTraceBack_ij = (int) uInsertPos - (int) j;
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306 assert(*ptrTraceBack_ij < 0);
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309 assert(ptrSortOrderA == &(SortOrderA[i]));
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310 assert(ptrFreqsA == &(FreqsA[i]));
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312 *ptrMCurr_j += scoreMax;
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313 assert(ptrMCurr_j == &(MCurr[j]));
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316 MPrev_j = *(++ptrMPrev_j);
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317 assert(ptrDPrev == &(DPrev[j]));
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318 SCORE d = *ptrDPrev;
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319 SCORE DNew = MPrev_j + scoreGapOpenAi;
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323 assert(ptrDeletePos == &uDeletePos[j]);
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326 assert(ptrDCurr + 1 == &(DCurr[j]));
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332 Rotate(MPrev, MCurr, MWork);
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333 Rotate(DPrev, DCurr, DWork);
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336 // Special case for i=uLengthA
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337 SCORE IPrev = MINUS_INFINITY;
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339 unsigned uInsertPos;
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341 for (unsigned j = 1; j < uLengthB; ++j)
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343 SCORE INew = MPrev[j-1] + GapOpenB[j];
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351 // Special case for i=uLengthA, j=uLengthB
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352 SCORE scoreMax = MPrev[uLengthB-1];
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353 int iTraceBack = 0;
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355 SCORE scoreD = DPrev[uLengthB-1] + GapCloseA[uLengthA-1];
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356 if (scoreD > scoreMax)
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359 iTraceBack = (int) uLengthA - (int) uDeletePos[uLengthB-1];
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362 SCORE scoreI = IPrev + GapCloseB[uLengthB-1];
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363 if (scoreI > scoreMax)
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366 iTraceBack = (int) uInsertPos - (int) uLengthB;
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369 TraceBack[uLengthA][uLengthB] = iTraceBack;
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371 TraceBackToPath(TraceBack, uLengthA, uLengthB, Path);
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