binaries/src/muscle/hydro.cpp

   1 #include "muscle.h"\r
   2 #include "profile.h"\r
   3 \r
   4 extern void TomHydro(ProfPos *Prof, unsigned Length);\r
   5 \r
   6 // Apply hydrophobicity heuristic to a profile\r
   7 void Hydro(ProfPos *Prof, unsigned uLength)\r
   8         {\r
   9         if (ALPHA_Amino != g_Alpha)\r
  10                 return;\r
  11 \r
  12         if (g_bTomHydro)\r
  13                 {\r
  14                 TomHydro(Prof, uLength);\r
  15                 return;\r
  16                 }\r
  17 \r
  18         if (0 == g_uHydrophobicRunLength)\r
  19                 return;\r
  20 \r
  21         if (uLength <= g_uHydrophobicRunLength)\r
  22                 return;\r
  23 \r
  24         unsigned uRunLength = 0;\r
  25         unsigned L2 = g_uHydrophobicRunLength/2;\r
  26         for (unsigned uColIndex = L2; uColIndex < uLength - L2; ++uColIndex)\r
  27                 {\r
  28                 ProfPos &PP = Prof[uColIndex];\r
  29                 bool bHydro = IsHydrophobic(PP.m_fcCounts);\r
  30                 if (bHydro)\r
  31                         {\r
  32                         ++uRunLength;\r
  33                         if (uRunLength >= g_uHydrophobicRunLength)\r
  34                                 {\r
  35                                 Prof[uColIndex-L2].m_scoreGapOpen *= (SCORE) g_dHydroFactor;\r
  36                                 Prof[uColIndex-L2].m_scoreGapClose *= (SCORE) g_dHydroFactor;\r
  37                                 }\r
  38                         }\r
  39                 else\r
  40                         uRunLength = 0;\r
  41                 }\r
  42         }\r