+++ /dev/null
-
-#ifndef __SCARNA_HPP__
-#define __SCARNA_HPP__
-
-#include <iostream>
-using namespace std;
-
-#define WORDLENGTH 2 /* default word length in stem candidates (SCs) */
-
-#define THR 0.01
-
-// the parameter trained by maximazing the sps of tRNA
-//#define MULTISCORE 9.870619 //multiple score with the constant.
-//#define MULTIRIBOSUM 0.452626 //multiple ribosum_score with the constant
-//#define MULTIPENALTY 24.263776 //multiple penalty with the constatnt
-//#define MULTISTACKING 45.208927 //multiple stacking energy with the constatnt
-
-/*
-#define MULTIRIBOSUM 1
-#define MULTIPENALTY 3.1
-#define MULTISCORE 3.7
-#define MULTISTACKING 0.1
-#define MULTIDELTASCORE 9.4
-#define MULTIDELTASTACKING 8.6
-*/
-/*
-#define MULTIRIBOSUM 1
-#define MULTIPENALTY 1.1162
-#define MULTISCORE 0.53299
-#define MULTISTACKING 4.25669
-#define MULTIDELTASCORE 1.17805
-#define MULTIDELTASTACKING 4.2016
-*/
-// new CRF DATA 550 sigma 1
-
-#define MULTIRIBOSUM 1
-#define MULTIPENALTY 1.82294
-#define MULTISCORE 0.250631
-#define MULTISTACKING 2.35517
-#define MULTIDELTASCORE 1.1781
-#define MULTIDELTASTACKING 2.45417
-
-/*
-#define MULTIRIBOSUM 1
-#define MULTIPENALTY 0.478054
-#define MULTISCORE 1.36322
-#define MULTISTACKING 4.96635
-#define MULTIDELTASCORE 1.14239
-#define MULTIDELTASTACKING 7.32992
-*/
-// CRF DATA 900 sigma 1
-/*
-#define MULTIRIBOSUM 1
-#define MULTIPENALTY 2.28364
-#define MULTISCORE 0.00945681
-#define MULTISTACKING 2.25357
-#define MULTIDELTASCORE 1.02201
-#define MULTIDELTASTACKING 2.21293
-*/
-
-/*
-#define RNAMATCHAA 506159
-#define RNAMATCHAT 359916
-#define RNAMATCHAG 451319
-#define RNAMATCHAC 390720
-#define RNAMATCHTT 398658
-#define RNAMATCHTG 377069
-#define RNAMATCHTC 378456
-#define RNAMATCHGG 554695
-#define RNAMATCHGC 419950
-#define RNAMATCHCC 479030
-#define GAPPENALTY 190947
-#define GAPEXTENTIONPENALTY -118817
-*/
-// RIBOSUM
-#define RNAMATCHAA 2.22
-#define RNAMATCHAT -1.39
-#define RNAMATCHAG -1.46
-#define RNAMATCHAC -1.86
-#define RNAMATCHTT 1.65
-#define RNAMATCHTG -1.74
-#define RNAMATCHTC -1.05
-#define RNAMATCHGG 1.03
-#define RNAMATCHGC -2.48
-#define RNAMATCHCC 1.16
-//#define GAPPENALTY 9.42 // 3default linear gap penalry in RNA sequence alignment
-//#define GAPPENALTY 9.18743
-//#define GAPPENALTY 5.00
-//#define GAPEXTENTIONPENALTY 7.15
-//#define GAPEXTENTIONPENALTY 9.62003
-
-#define GAPPENALTY 5
-#define GAPEXTENTIONPENALTY 2.5
-//#define GAPPENALTY 8.08875
-//#define GAPEXTENTIONPENALTY 3.89655
-
-#define REFINEMENTREPS 0
-#define SCSLENGTH 2
-#define BASEPROBTHRESHOLD 0.01
-#define BASEPAIRCONST 6
-#define BANDWIDTH 500
-#define USERFOLD false
-
-extern float RNA_Match_AA;
-extern float RNA_Match_AT;
-extern float RNA_Match_AG;
-extern float RNA_Match_AC;
-extern float RNA_Match_TT;
-extern float RNA_Match_TG;
-extern float RNA_Match_TC;
-extern float RNA_Match_GG;
-extern float RNA_Match_GC;
-extern float RNA_Match_CC;
-extern float RNA_Gap_Penalty;
-extern float RNA_Gap_Extension;
-
-extern int numIterativeRefinementReps;
-extern bool PostProcessAlignment;
-extern int scsLength;
-extern float BaseProbThreshold;
-extern float BasePairConst;
-
-#endif /*__SCARNA_HPP__*/
-