binaries/src/muscle/scorepp.cpp

   1 #include "muscle.h"\r
   2 #include "profile.h"\r
   3 \r
   4 char ConsensusChar(const ProfPos &PP)\r
   5         {\r
   6         unsigned uMostCommonLetter = 0;\r
   7         FCOUNT fcMostCommon = PP.m_fcCounts[0];\r
   8         bool bMoreThanOneLetter = false;\r
   9         bool bAnyLetter = false;\r
  10         for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter)\r
  11                 {\r
  12                 const FCOUNT fc = PP.m_fcCounts[uLetter];\r
  13                 if (fc > 0)\r
  14                         {\r
  15                         if (bAnyLetter)\r
  16                                 bMoreThanOneLetter = true;\r
  17                         bAnyLetter = true;\r
  18                         }\r
  19                 if (fc > fcMostCommon)\r
  20                         {\r
  21                         uMostCommonLetter = uLetter;\r
  22                         fcMostCommon = fc;\r
  23                         }\r
  24                 }\r
  25         if (!bAnyLetter)\r
  26                 return '-';\r
  27         char c = LetterToChar(uMostCommonLetter);\r
  28         if (bMoreThanOneLetter)\r
  29                 return UnalignChar(c);\r
  30         return c;\r
  31         }\r
  32 \r
  33 SCORE ScoreProfPos2LA(const ProfPos &PPA, const ProfPos &PPB)\r
  34         {\r
  35         SCORE Score = 0;\r
  36         for (unsigned n = 0; n < 20; ++n)\r
  37                 {\r
  38                 const unsigned uLetter = PPA.m_uSortOrder[n];\r
  39                 const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];\r
  40                 if (0 == fcLetter)\r
  41                         break;\r
  42                 Score += fcLetter*PPB.m_AAScores[uLetter];\r
  43                 }\r
  44         if (0 == Score)\r
  45                 return -2.5;\r
  46         SCORE logScore = logf(Score);\r
  47         return (SCORE) ((logScore - g_scoreCenter)*(PPA.m_fOcc * PPB.m_fOcc));\r
  48         }\r
  49 \r
  50 SCORE ScoreProfPos2NS(const ProfPos &PPA, const ProfPos &PPB)\r
  51         {\r
  52         SCORE Score = 0;\r
  53         for (unsigned n = 0; n < 20; ++n)\r
  54                 {\r
  55                 const unsigned uLetter = PPA.m_uSortOrder[n];\r
  56                 const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];\r
  57                 if (0 == fcLetter)\r
  58                         break;\r
  59                 Score += fcLetter*PPB.m_AAScores[uLetter];\r
  60                 }\r
  61         return Score - g_scoreCenter;\r
  62         }\r
  63 \r
  64 SCORE ScoreProfPos2SP(const ProfPos &PPA, const ProfPos &PPB)\r
  65         {\r
  66         SCORE Score = 0;\r
  67         for (unsigned n = 0; n < 20; ++n)\r
  68                 {\r
  69                 const unsigned uLetter = PPA.m_uSortOrder[n];\r
  70                 const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];\r
  71                 if (0 == fcLetter)\r
  72                         break;\r
  73                 Score += fcLetter*PPB.m_AAScores[uLetter];\r
  74                 }\r
  75         return Score - g_scoreCenter;\r
  76         }\r
  77 \r
  78 SCORE ScoreProfPos2SPN(const ProfPos &PPA, const ProfPos &PPB)\r
  79         {\r
  80         SCORE Score = 0;\r
  81         for (unsigned n = 0; n < 4; ++n)\r
  82                 {\r
  83                 const unsigned uLetter = PPA.m_uSortOrder[n];\r
  84                 const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];\r
  85                 if (0 == fcLetter)\r
  86                         break;\r
  87                 Score += fcLetter*PPB.m_AAScores[uLetter];\r
  88                 }\r
  89         return Score - g_scoreCenter;\r
  90         }\r
  91 \r
  92 SCORE ScoreProfPos2(const ProfPos &PPA, const ProfPos &PPB)\r
  93         {\r
  94         if (PPSCORE_SP == g_PPScore)\r
  95                 return ScoreProfPos2NS(PPA, PPB);\r
  96         else if (PPSCORE_LE == g_PPScore)\r
  97                 return ScoreProfPos2LA(PPA, PPB);\r
  98         else if (PPSCORE_SV == g_PPScore)\r
  99                 return ScoreProfPos2SP(PPA, PPB);\r
 100         else if (PPSCORE_SPN == g_PPScore)\r
 101                 return ScoreProfPos2SPN(PPA, PPB);\r
 102         Quit("Invalid g_PPScore");\r
 103         return 0;\r
 104         }\r