binaries/src/mafft/extensions/mxscarna_src/GlobalParameters.cpp

   1 //////////////////////////////////////////////////////////////
   2 // GlobalParameters.cpp
   3 // This file include Global Parameters, command line options, etc.
   4 //////////////////////////////////////////////////////////////
   5
   6 #include "scarna.hpp"
   7
   8 // These paramenters are defined in scarna.hpp
   9
  10 float RNA_Match_AA      = RNAMATCHAA;
  11 float RNA_Match_AT      = RNAMATCHAT;
  12 float RNA_Match_AG      = RNAMATCHAG;
  13 float RNA_Match_AC      = RNAMATCHAC;
  14 float RNA_Match_TT      = RNAMATCHTT;
  15 float RNA_Match_TG      = RNAMATCHTG;
  16 float RNA_Match_TC      = RNAMATCHTC;
  17 float RNA_Match_GG      = RNAMATCHGG;
  18 float RNA_Match_GC      = RNAMATCHGC;
  19 float RNA_Match_CC      = RNAMATCHCC;
  20 float RNA_Gap_Penalty   = GAPPENALTY;
  21 float RNA_Gap_Extension = GAPEXTENTIONPENALTY;
  22
  23 int   numIterativeRefinementReps = REFINEMENTREPS;
  24 bool  PostProcessAlignment = false;
  25 int   scsLength = SCSLENGTH;
  26 float BaseProbThreshold = BASEPROBTHRESHOLD;
  27 float BasePairConst     = BASEPAIRCONST;