binaries/src/muscle/distpwkimura.cpp

   1 #include "muscle.h"\r
   2 #include "distfunc.h"\r
   3 #include "msa.h"\r
   4 #include "seqvect.h"\r
   5 #include "pwpath.h"\r
   6 \r
   7 void DistPWKimura(const SeqVect &v, DistFunc &DF)\r
   8         {\r
   9         SEQWEIGHT SeqWeightSave = GetSeqWeightMethod();\r
  10         SetSeqWeightMethod(SEQWEIGHT_Henikoff);\r
  11 \r
  12         const unsigned uSeqCount = v.Length();\r
  13         DF.SetCount(uSeqCount);\r
  14 \r
  15         const unsigned uPairCount = (uSeqCount*(uSeqCount + 1))/2;\r
  16         unsigned uCount = 0;\r
  17         SetProgressDesc("PWKimura distance");\r
  18         for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)\r
  19                 {\r
  20                 const Seq &s1 = v.GetSeq(uSeqIndex1);\r
  21                 MSA msa1;\r
  22                 msa1.FromSeq(s1);\r
  23                 for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqIndex1; ++uSeqIndex2)\r
  24                         {\r
  25                         if (0 == uCount%20)\r
  26                                 Progress(uCount, uPairCount);\r
  27                         ++uCount;\r
  28                         const Seq &s2 = v.GetSeq(uSeqIndex2);\r
  29                         MSA msa2;\r
  30                         msa2.FromSeq(s2);\r
  31                 \r
  32                         PWPath Path;\r
  33                         MSA msaOut;\r
  34                         AlignTwoMSAs(msa1, msa2, msaOut, Path, false, false);\r
  35 \r
  36                         double dPctId = msaOut.GetPctIdentityPair(0, 1);\r
  37                         float f = (float) KimuraDist(dPctId);\r
  38 \r
  39                         DF.SetDist(uSeqIndex1, uSeqIndex2, f);\r
  40                         }\r
  41                 }\r
  42         ProgressStepsDone();\r
  43 \r
  44         SetSeqWeightMethod(SeqWeightSave);\r
  45         }\r