binaries/src/muscle/fastdist.cpp

   1 #include "muscle.h"\r
   2 #include "distfunc.h"\r
   3 #include "seqvect.h"\r
   4 \r
   5 void DistPWScoreDist(const SeqVect &v, DistFunc &DF);\r
   6 \r
   7 void DistUnaligned(const SeqVect &v, DISTANCE DistMethod, DistFunc &DF)\r
   8         {\r
   9         const unsigned uSeqCount = v.Length();\r
  10 \r
  11         switch (DistMethod)\r
  12                 {\r
  13         case DISTANCE_Kmer6_6:\r
  14                 DistKmer6_6(v, DF);\r
  15                 break;\r
  16 \r
  17         case DISTANCE_Kmer20_3:\r
  18                 DistKmer20_3(v, DF);\r
  19                 break;\r
  20 \r
  21         case DISTANCE_Kmer20_4:\r
  22                 FastDistKmer(v, DF);\r
  23                 break;\r
  24 \r
  25         case DISTANCE_Kbit20_3:\r
  26                 DistKbit20_3(v, DF);\r
  27                 break;\r
  28 \r
  29         case DISTANCE_Kmer4_6:\r
  30                 DistKmer4_6(v, DF);\r
  31                 break;\r
  32 \r
  33         case DISTANCE_PWKimura:\r
  34                 DistPWKimura(v, DF);\r
  35                 break;\r
  36 \r
  37         case DISTANCE_PWScoreDist:\r
  38                 DistPWScoreDist(v, DF);\r
  39                 break;\r
  40 \r
  41         default:\r
  42                 Quit("DistUnaligned, unsupported distance method %d", DistMethod);\r
  43                 }\r
  44 \r
  45 //      const char **SeqNames = (const char **) malloc(uSeqCount*sizeof(char *));\r
  46         for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
  47                 {\r
  48                 const Seq &s = *(v[uSeqIndex]);\r
  49 \r
  50                 const char *ptrName = s.GetName();\r
  51                 unsigned uId = s.GetId();\r
  52 \r
  53                 DF.SetName(uSeqIndex, ptrName);\r
  54                 DF.SetId(uSeqIndex, uId);\r
  55                 }\r
  56         }\r