uchime_src/getparents.cpp

   1 #include "myutils.h"\r
   2 #include "chime.h"\r
   3 #include "ultra.h"\r
   4 #include <set>\r
   5 \r
   6 void AddTargets(Ultra &U, const SeqData &Query, set<unsigned> &TargetIndexes);\r
   7 \r
   8 void GetChunkInfo(unsigned L, unsigned &Length, vector<unsigned> &Los)\r
   9         {\r
  10         Los.clear();\r
  11 \r
  12         if (L <= opt_minchunk)\r
  13                 {\r
  14                 Length = L;\r
  15                 Los.push_back(0);\r
  16                 return;\r
  17                 }\r
  18 \r
  19         Length = (L - 1)/opt_chunks + 1;\r
  20         if (Length < opt_minchunk)\r
  21                 Length = opt_minchunk;\r
  22 \r
  23         unsigned Lo = 0;\r
  24         for (;;)\r
  25                 {\r
  26                 if (Lo + Length >= L)\r
  27                         {\r
  28                         Lo = L - Length - 1;\r
  29                         Los.push_back(Lo);\r
  30                         return;\r
  31                         }\r
  32                 Los.push_back(Lo);\r
  33                 Lo += Length;\r
  34                 }\r
  35         }\r
  36 \r
  37 void GetCandidateParents(Ultra &U, const SeqData &QSD, float AbQ,\r
  38   vector<unsigned> &Parents)\r
  39         {\r
  40         Parents.clear();\r
  41 \r
  42         set<unsigned> TargetIndexes;\r
  43 \r
  44         unsigned QL = QSD.L;\r
  45 \r
  46         SeqData QuerySD = QSD;\r
  47 \r
  48         unsigned ChunkLength;\r
  49         vector<unsigned> ChunkLos;\r
  50         GetChunkInfo(QL, ChunkLength, ChunkLos);\r
  51         unsigned ChunkCount = SIZE(ChunkLos);\r
  52         for (unsigned ChunkIndex = 0; ChunkIndex < ChunkCount; ++ChunkIndex)\r
  53                 {\r
  54                 unsigned Lo = ChunkLos[ChunkIndex];\r
  55                 asserta(Lo + ChunkLength <= QL);\r
  56 \r
  57                 const byte *Chunk = QSD.Seq + Lo;\r
  58 \r
  59         // THIS MESSES UP --self!!\r
  60                 //char Prefix[32];\r
  61                 //sprintf(Prefix, "%u|", Lo);\r
  62                 //string ChunkLabel = string(Prefix) + string(QSD.Label);\r
  63 \r
  64                 //QuerySD.Label = ChunkLabel.c_str();\r
  65                 QuerySD.Seq = Chunk;\r
  66                 QuerySD.L = ChunkLength;\r
  67 \r
  68                 AddTargets(U, QuerySD, TargetIndexes);\r
  69 \r
  70                 Lo += ChunkLength;\r
  71                 }\r
  72 \r
  73         for (set<unsigned>::const_iterator p = TargetIndexes.begin();\r
  74           p != TargetIndexes.end(); ++p)\r
  75                 {\r
  76                 unsigned TargetIndex = *p;\r
  77                 bool Accept = true;\r
  78                 if (AbQ > 0.0f)\r
  79                         {\r
  80                         const char *TargetLabel = U.GetSeedLabel(TargetIndex);\r
  81                         float AbT = GetAbFromLabel(string(TargetLabel));\r
  82                         if (AbT > 0.0f && AbT < opt_abskew*AbQ)\r
  83                                 Accept = false;\r
  84                         }\r
  85 \r
  86                 if (Accept)\r
  87                         Parents.push_back(TargetIndex);\r
  88                 }\r
  89         }\r