new mafft v 6.857 with extensions

[jabaws.git] / binaries / src / mafft / extensions / mxscarna_src / scarna.hpp

diff --git a/binaries/src/mafft/extensions/mxscarna_src/scarna.hpp b/binaries/src/mafft/extensions/mxscarna_src/scarna.hpp
new file mode 100644 (file)
index 0000000..ac58548
--- /dev/null
+++ b/binaries/src/mafft/extensions/mxscarna_src/scarna.hpp
@@ -0,0 +1,124 @@
+
+#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__*/
+