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[jabaws.git] / website / archive / binaries / mac / src / muscle / spfast.cpp
diff --git a/website/archive/binaries/mac/src/muscle/spfast.cpp b/website/archive/binaries/mac/src/muscle/spfast.cpp
deleted file mode 100644 (file)
index 51e0dba..0000000
--- a/website/archive/binaries/mac/src/muscle/spfast.cpp
+++ /dev/null
@@ -1,269 +0,0 @@
-#include "muscle.h"\r
-#include "profile.h"\r
-\r
-#define TRACE  0\r
-\r
-enum\r
-       {\r
-       LL = 0,\r
-       LG = 1,\r
-       GL = 2,\r
-       GG = 3,\r
-       };\r
-\r
-static const char *GapTypeToStr(int GapType)\r
-       {\r
-       switch (GapType)\r
-               {\r
-       case LL: return "LL";\r
-       case LG: return "LG";\r
-       case GL: return "GL";\r
-       case GG: return "GG";\r
-               }\r
-       Quit("Invalid gap type");\r
-       return "?";\r
-       }\r
-\r
-static SCORE GapScoreMatrix[4][4];\r
-\r
-static void InitGapScoreMatrix()\r
-       {\r
-       const SCORE t = (SCORE) 0.2;\r
-\r
-       GapScoreMatrix[LL][LL] = 0;\r
-       GapScoreMatrix[LL][LG] = g_scoreGapOpen;\r
-       GapScoreMatrix[LL][GL] = 0;\r
-       GapScoreMatrix[LL][GG] = 0;\r
-\r
-       GapScoreMatrix[LG][LL] = g_scoreGapOpen;\r
-       GapScoreMatrix[LG][LG] = 0;\r
-       GapScoreMatrix[LG][GL] = g_scoreGapOpen;\r
-       GapScoreMatrix[LG][GG] = t*g_scoreGapOpen;      // approximation!\r
-\r
-       GapScoreMatrix[GL][LL] = 0;\r
-       GapScoreMatrix[GL][LG] = g_scoreGapOpen;\r
-       GapScoreMatrix[GL][GL] = 0;\r
-       GapScoreMatrix[GL][GG] = 0;\r
-\r
-       GapScoreMatrix[GG][LL] = 0;\r
-       GapScoreMatrix[GG][LG] = t*g_scoreGapOpen;      // approximation!\r
-       GapScoreMatrix[GG][GL] = 0;\r
-       GapScoreMatrix[GG][GG] = 0;\r
-\r
-       for (int i = 0; i < 4; ++i)\r
-               for (int j = 0; j < i; ++j)\r
-                       if (GapScoreMatrix[i][j] != GapScoreMatrix[j][i])\r
-                               Quit("GapScoreMatrix not symmetrical");\r
-       }\r
-\r
-static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)\r
-       {\r
-       SCORE Sum = 0;\r
-       const unsigned uSeqCount = msa.GetSeqCount();\r
-       for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)\r
-               {\r
-               const WEIGHT w1 = msa.GetSeqWeight(uSeqIndex1);\r
-               unsigned uLetter1 = msa.GetLetterEx(uSeqIndex1, uColIndex);\r
-               if (uLetter1 >= 20)\r
-                       continue;\r
-               for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqIndex1; ++uSeqIndex2)\r
-                       {\r
-                       const WEIGHT w2 = msa.GetSeqWeight(uSeqIndex2);\r
-                       unsigned uLetter2 = msa.GetLetterEx(uSeqIndex2, uColIndex);\r
-                       if (uLetter2 >= 20)\r
-                               continue;\r
-                       SCORE t = w1*w2*(*g_ptrScoreMatrix)[uLetter1][uLetter2];\r
-#if    TRACE\r
-                       Log("Check %c %c w1=%.3g w2=%.3g Mx=%.3g t=%.3g\n",\r
-                         LetterToCharAmino(uLetter1),\r
-                         LetterToCharAmino(uLetter2),\r
-                         w1,\r
-                         w2,\r
-                         (*g_ptrScoreMatrix)[uLetter1][uLetter2],\r
-                         t);\r
-#endif\r
-                       Sum += t;\r
-                       }\r
-               }\r
-       return Sum;\r
-       }\r
-\r
-static SCORE SPGapFreqs(const FCOUNT Freqs[])\r
-       {\r
-#if TRACE\r
-       Log("Freqs=");\r
-       for (unsigned i = 0; i < 4; ++i)\r
-               if (Freqs[i] != 0)\r
-                       Log(" %s=%.3g", GapTypeToStr(i), Freqs[i]);\r
-       Log("\n");\r
-#endif\r
-\r
-       SCORE TotalOffDiag = 0;\r
-       SCORE TotalDiag = 0;\r
-       for (unsigned i = 0; i < 4; ++i)\r
-               {\r
-               const FCOUNT fi = Freqs[i];\r
-               if (0 == fi)\r
-                       continue;\r
-               const float *Row = GapScoreMatrix[i];\r
-               SCORE diagt = fi*fi*Row[i];\r
-               TotalDiag += diagt;\r
-#if    TRACE\r
-               Log("SPFGaps %s %s + Mx=%.3g TotalDiag += %.3g\n",\r
-                 GapTypeToStr(i),\r
-                 GapTypeToStr(i),\r
-                 Row[i],\r
-                 diagt);\r
-#endif\r
-               SCORE Sum = 0;\r
-               for (unsigned j = 0; j < i; ++j)\r
-                       {\r
-                       SCORE t = Freqs[j]*Row[j];\r
-#if    TRACE\r
-                       if (Freqs[j] != 0)\r
-                               Log("SPFGaps %s %s + Mx=%.3g Sum += %.3g\n",\r
-                                 GapTypeToStr(i),\r
-                                 GapTypeToStr(j),\r
-                                 Row[j],\r
-                                 fi*t);\r
-#endif\r
-                       Sum += t;\r
-                       }\r
-               TotalOffDiag += fi*Sum;\r
-               }\r
-#if TRACE\r
-       Log("SPFGap TotalOffDiag=%.3g + TotalDiag=%.3g = %.3g\n",\r
-         TotalOffDiag, TotalDiag, TotalOffDiag + TotalDiag);\r
-#endif\r
-       return TotalOffDiag*2 + TotalDiag;\r
-       }\r
-\r
-static SCORE SPFreqs(const FCOUNT Freqs[])\r
-       {\r
-#if TRACE\r
-       Log("Freqs=");\r
-       for (unsigned i = 0; i < 20; ++i)\r
-               if (Freqs[i] != 0)\r
-                       Log(" %c=%.3g", LetterToCharAmino(i), Freqs[i]);\r
-       Log("\n");\r
-#endif\r
-\r
-       SCORE TotalOffDiag = 0;\r
-       SCORE TotalDiag = 0;\r
-       for (unsigned i = 0; i < 20; ++i)\r
-               {\r
-               const FCOUNT fi = Freqs[i];\r
-               if (0 == fi)\r
-                       continue;\r
-               const float *Row = (*g_ptrScoreMatrix)[i];\r
-               SCORE diagt = fi*fi*Row[i];\r
-               TotalDiag += diagt;\r
-#if    TRACE\r
-               Log("SPF %c %c + Mx=%.3g TotalDiag += %.3g\n",\r
-                 LetterToCharAmino(i),\r
-                 LetterToCharAmino(i),\r
-                 Row[i],\r
-                 diagt);\r
-#endif\r
-               SCORE Sum = 0;\r
-               for (unsigned j = 0; j < i; ++j)\r
-                       {\r
-                       SCORE t = Freqs[j]*Row[j];\r
-#if    TRACE\r
-                       if (Freqs[j] != 0)\r
-                               Log("SPF %c %c + Mx=%.3g Sum += %.3g\n",\r
-                                 LetterToCharAmino(i),\r
-                                 LetterToCharAmino(j),\r
-                                 Row[j],\r
-                                 fi*t);\r
-#endif\r
-                       Sum += t;\r
-                       }\r
-               TotalOffDiag += fi*Sum;\r
-               }\r
-#if TRACE\r
-       Log("SPF TotalOffDiag=%.3g + TotalDiag=%.3g = %.3g\n",\r
-         TotalOffDiag, TotalDiag, TotalOffDiag + TotalDiag);\r
-#endif\r
-       return TotalOffDiag*2 + TotalDiag;\r
-       }\r
-\r
-static SCORE ObjScoreSPCol(const MSA &msa, unsigned uColIndex)\r
-       {\r
-       FCOUNT Freqs[20];\r
-       FCOUNT GapFreqs[4];\r
-\r
-       memset(Freqs, 0, sizeof(Freqs));\r
-       memset(GapFreqs, 0, sizeof(GapFreqs));\r
-\r
-       const unsigned uSeqCount = msa.GetSeqCount();\r
-#if    TRACE\r
-       Log("Weights=");\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               Log(" %u=%.3g", uSeqIndex, msa.GetSeqWeight(uSeqIndex));\r
-       Log("\n");\r
-#endif\r
-       SCORE SelfOverCount = 0;\r
-       SCORE GapSelfOverCount = 0;\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               WEIGHT w = msa.GetSeqWeight(uSeqIndex);\r
-\r
-               bool bGapThisCol = msa.IsGap(uSeqIndex, uColIndex);\r
-               bool bGapPrevCol = (uColIndex == 0 ? false : msa.IsGap(uSeqIndex, uColIndex - 1));\r
-               int GapType = bGapThisCol + 2*bGapPrevCol;\r
-               assert(GapType >= 0 && GapType < 4);\r
-               GapFreqs[GapType] += w;\r
-               SCORE gapt = w*w*GapScoreMatrix[GapType][GapType];\r
-               GapSelfOverCount += gapt;\r
-\r
-               if (bGapThisCol)\r
-                       continue;\r
-               unsigned uLetter = msa.GetLetterEx(uSeqIndex, uColIndex);\r
-               if (uLetter >= 20)\r
-                       continue;\r
-               Freqs[uLetter] += w;\r
-               SCORE t = w*w*(*g_ptrScoreMatrix)[uLetter][uLetter];\r
-#if    TRACE\r
-               Log("FastCol compute freqs & SelfOverCount %c w=%.3g M=%.3g SelfOverCount += %.3g\n",\r
-                 LetterToCharAmino(uLetter), w, (*g_ptrScoreMatrix)[uLetter][uLetter], t);\r
-#endif\r
-               SelfOverCount += t;\r
-               }\r
-       SCORE SPF = SPFreqs(Freqs);\r
-       SCORE Col = SPF - SelfOverCount;\r
-\r
-       SCORE SPFGaps = SPGapFreqs(GapFreqs);\r
-       SCORE ColGaps = SPFGaps - GapSelfOverCount;\r
-#if    TRACE\r
-       Log("SPF=%.3g - SelfOverCount=%.3g = %.3g\n", SPF, SelfOverCount, Col);\r
-       Log("SPFGaps=%.3g - GapsSelfOverCount=%.3g = %.3g\n", SPFGaps, GapSelfOverCount, ColGaps);\r
-#endif\r
-       return Col + ColGaps;\r
-       }\r
-\r
-SCORE ObjScoreSPDimer(const MSA &msa)\r
-       {\r
-       static bool bGapScoreMatrixInit = false;\r
-       if (!bGapScoreMatrixInit)\r
-               InitGapScoreMatrix();\r
-\r
-       SCORE Total = 0;\r
-       const unsigned uSeqCount = msa.GetSeqCount();\r
-       const unsigned uColCount = msa.GetColCount();\r
-       for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)\r
-               {\r
-               SCORE Col = ObjScoreSPCol(msa, uColIndex);\r
-#if    TRACE\r
-               {\r
-               SCORE ColCheck = SPColBrute(msa, uColIndex);\r
-               Log("FastCol=%.3g CheckCol=%.3g\n", Col, ColCheck);\r
-               }\r
-#endif\r
-               Total += Col;\r
-               }\r
-#if TRACE\r
-       Log("Total/2 = %.3g (final result from fast)\n", Total/2);\r
-#endif\r
-       return Total/2;\r
-       }\r