binaries/src/muscle/msadist.h

   1 #ifndef MSADist_h\r
   2 #define MSADist_h\r
   3 \r
   4 #include <math.h>\r
   5 \r
   6 double GetScoreDist(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2);\r
   7 \r
   8 class MSADist\r
   9         {\r
  10 public:\r
  11         MSADist(DISTANCE Distance)\r
  12                 {\r
  13                 m_Distance = Distance;\r
  14                 }\r
  15 \r
  16         double ComputeDist(const MSA &msa, unsigned uSeqIndex1, unsigned uSeqIndex2)\r
  17                 {\r
  18                 if (m_Distance == DISTANCE_ScoreDist)\r
  19                         return GetScoreDist(msa, uSeqIndex1, uSeqIndex2);\r
  20 \r
  21                 double dPctId = msa.GetPctIdentityPair(uSeqIndex1, uSeqIndex2);\r
  22                 switch(m_Distance)\r
  23                         {\r
  24                 case DISTANCE_PctIdKimura:\r
  25                         return KimuraDist(dPctId);\r
  26                 case DISTANCE_PctIdLog:\r
  27                         if (dPctId < 0.05)\r
  28                                 dPctId = 0.05;\r
  29                         return -log(dPctId);\r
  30                         }\r
  31                 Quit("MSADist::ComputeDist, invalid DISTANCE_%u", m_Distance);\r
  32                 return 0;\r
  33                 }\r
  34 \r
  35 private:\r
  36         DISTANCE m_Distance;\r
  37         };\r
  38 \r
  39 #endif  // MSADist_h\r