--- /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__*/
+