binaries/src/muscle/distcalc.cpp

   1 #include "muscle.h"\r
   2 #include "distfunc.h"\r
   3 #include "distcalc.h"\r
   4 #include "msa.h"\r
   5 \r
   6 void DistCalcDF::Init(const DistFunc &DF)\r
   7         {\r
   8         m_ptrDF = &DF;\r
   9         }\r
  10 \r
  11 void DistCalcDF::CalcDistRange(unsigned i, dist_t Dist[]) const\r
  12         {\r
  13         for (unsigned j = 0; j < i; ++j)\r
  14                 Dist[j] = m_ptrDF->GetDist(i, j);\r
  15         }\r
  16 \r
  17 unsigned DistCalcDF::GetCount() const\r
  18         {\r
  19         return m_ptrDF->GetCount();\r
  20         }\r
  21 \r
  22 unsigned DistCalcDF::GetId(unsigned i) const\r
  23         {\r
  24         return m_ptrDF->GetId(i);\r
  25         }\r
  26 \r
  27 const char *DistCalcDF::GetName(unsigned i) const\r
  28         {\r
  29         return m_ptrDF->GetName(i);\r
  30         }\r
  31 \r
  32 void DistCalcMSA::Init(const MSA &msa, DISTANCE Distance)\r
  33         {\r
  34         m_ptrMSA = &msa;\r
  35         m_Distance = Distance;\r
  36         }\r
  37 \r
  38 void DistCalcMSA::CalcDistRange(unsigned i, dist_t Dist[]) const\r
  39         {\r
  40         for (unsigned j = 0; j < i; ++j)\r
  41                 {\r
  42                 switch (m_Distance)\r
  43                         {\r
  44                 case DISTANCE_PctIdKimura:\r
  45                         {\r
  46                         const float PctId = (float) m_ptrMSA->GetPctIdentityPair(i, j);\r
  47                         Dist[j] = (float) KimuraDist(PctId);\r
  48                         break;\r
  49                         }\r
  50                 case DISTANCE_PctIdLog:\r
  51                         {\r
  52                         const float PctId = (float) m_ptrMSA->GetPctIdentityPair(i, j);\r
  53                         Dist[j] = (float) PctIdToMAFFTDist(PctId);\r
  54                         break;\r
  55                         }\r
  56                 case DISTANCE_ScoreDist:\r
  57                         {\r
  58                         double GetScoreDist(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2);\r
  59                         Dist[j] = (float) GetScoreDist(*m_ptrMSA, i, j);\r
  60                         continue;\r
  61                         }\r
  62                 case DISTANCE_Edit:\r
  63                         {\r
  64                         const float PctId = (float) m_ptrMSA->GetPctIdentityPair(i, j);\r
  65                         if (PctId > 1.0)\r
  66                                 Quit("Internal error, DISTANCE_Edit, pct id=%.3g", PctId);\r
  67                         Dist[j] = (float) 1.0 - PctId;\r
  68                         break;\r
  69                         }\r
  70                 default:\r
  71                         Quit("DistCalcMSA: Invalid DISTANCE_%u", m_Distance);\r
  72                         }\r
  73                 }\r
  74         }\r
  75 \r
  76 unsigned DistCalcMSA::GetCount() const\r
  77         {\r
  78         return m_ptrMSA->GetSeqCount();\r
  79         }\r
  80 \r
  81 unsigned DistCalcMSA::GetId(unsigned i) const\r
  82         {\r
  83         return m_ptrMSA->GetSeqId(i);\r
  84         }\r
  85 \r
  86 const char *DistCalcMSA::GetName(unsigned i) const\r
  87         {\r
  88         return m_ptrMSA->GetSeqName(i);\r
  89         }\r