Removing old version of mafft to replace with the new

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