+++ /dev/null
-//////////////////////////////////////////////////////////////
-// GlobalParameters.cpp
-// This file include Global Parameters, command line options, etc.
-//////////////////////////////////////////////////////////////
-
-#include "scarna.hpp"
-
-// These paramenters are defined in scarna.hpp
-
-float RNA_Match_AA = RNAMATCHAA;
-float RNA_Match_AT = RNAMATCHAT;
-float RNA_Match_AG = RNAMATCHAG;
-float RNA_Match_AC = RNAMATCHAC;
-float RNA_Match_TT = RNAMATCHTT;
-float RNA_Match_TG = RNAMATCHTG;
-float RNA_Match_TC = RNAMATCHTC;
-float RNA_Match_GG = RNAMATCHGG;
-float RNA_Match_GC = RNAMATCHGC;
-float RNA_Match_CC = RNAMATCHCC;
-float RNA_Gap_Penalty = GAPPENALTY;
-float RNA_Gap_Extension = GAPEXTENTIONPENALTY;
-
-int numIterativeRefinementReps = REFINEMENTREPS;
-bool PostProcessAlignment = false;
-int scsLength = SCSLENGTH;
-float BaseProbThreshold = BASEPROBTHRESHOLD;
-float BasePairConst = BASEPAIRCONST;