remove mafft extensions - we do not support them

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

diff --git a/binaries/src/mafft/extensions/mxscarna_src/vienna/energy_param.hpp b/binaries/src/mafft/extensions/mxscarna_src/vienna/energy_param.hpp
deleted file mode 100644 (file)
index b6bcd4c..0000000
--- a/binaries/src/mafft/extensions/mxscarna_src/vienna/energy_param.hpp
+++ /dev/null
@@ -1,111 +0,0 @@
-/* 
-    Current free energy parameters are summarized in:
-
-    D.H.Mathews, J. Sabina, M. ZUker, D.H. Turner
-    "Expanded sequence dependence of thermodynamic parameters improves
-    prediction of RNA secondary structure"
-    JMB, 288, pp 911-940, 1999
-
-    Enthalpies taken from:
-    
-    A. Walter, D Turner, J Kim, M Lyttle, P M"uller, D Mathews, M Zuker
-    "Coaxial stckaing of helices enhances binding of oligoribonucleotides.."
-    PNAS, 91, pp 9218-9222, 1994
-    
-    D.H. Turner, N. Sugimoto, and S.M. Freier.
-    "RNA Structure Prediction",
-    Ann. Rev. Biophys. Biophys. Chem. 17, 167-192, 1988.
-
-    John A.Jaeger, Douglas H.Turner, and Michael Zuker.
-    "Improved predictions of secondary structures for RNA",
-    PNAS, 86, 7706-7710, October 1989.
-    
-    L. He, R. Kierzek, J. SantaLucia, A.E. Walter, D.H. Turner
-    "Nearest-Neughbor Parameters for GU Mismatches...."
-    Biochemistry 1991, 30 11124-11132
-
-    A.E. Peritz, R. Kierzek, N, Sugimoto, D.H. Turner
-    "Thermodynamic Study of Internal Loops in Oligoribonucleotides..."
-    Biochemistry 1991, 30, 6428--6435
-
-    
-*/
-
-#ifndef ENERGY_PARAM_H
-#define ENERGY_PARAM_H
-
-#include <iostream>
-#include <cstdlib> // by katoh
-
-using namespace std;
-namespace MXSCARNA {
-class energy_param {
-
-    static const int    INF;
-    static const int    NST;
-    static const int    DEF;
-
-    static const double lxc37; /* parameter for logarithmic loop
-                             energy extrapolation            */
-    static const int stack37[8][8];
-    static const int enthalpies[8][8];
-    static const int oldhairpin37[31];
-    static const int hairpin37[31];
-    static const int oldbulge37[31];
-    static const int bulge37[31];
-    static const int oldinternal_loop37[31];
-    static const int internal_loop37[31];
-    static const int mismatchI37[8][5][5];
-    static const int mismatchH37[8][5][5];
-    static const int mism_H[8][5][5];
-    static const int dangle5_37[8][5];
-    static const int dangle3_37[8][5];
-    static const int dangle3_H[8][5];
-    static const int dangle5_H[8][5];
-    static const int ML_BASE37;
-    static const int ML_closing37;
-    static const int ML_intern37;
-    static const int MAX_NINIO;
-    static const int F_ninio37[5];
-    static const char Tetraloops[1400];
-    static const char Tetrastrings[30][7];
-    static const int TETRA_ENERGY37[200];
-    static const int TETRA_ENTH37;
-    static const int TerminalAU;
-    static const int DuplexInit;
-
-    static const int int11_37[8][8][5][5];
-    static const int int11_H[8][8][5][5];
-    static const int int21_37[8][8][5][5][5];
-    static const int int21_H[8][8][5][5][5];
-    static const int int22_37[8][8][5][5][5][5];
-    static const int int22_H[8][8][5][5][5][5];
-
-    int convertPairType(int type);
-    int convertBaseType(int type);
-    int convertLeftType(int type);
-    int convertRightType(int type);
- 
- public:
-    int getMaxNinio();
-    int getNinio(int i);
-    int getDangle5(int i, int j);
-    int getDangle3(int i, int j);
-    int getHairpin(int i);
-    int getInternalLoop(int i);
-    int getBulge(int i);
-    const char *getTetraLoop(int i);
-    int getTetraLoopEnergy(int i);
-    int getStack(int i, int j);
-    int getTstackH(int i, int j);
-    int getTstackI(int i, int j);
-    int getInt11(int i, int j, int k);
-    int getInt21(int i, int j, int k, int l);
-    int getInt22(int i, int j, int k, int l);
-    int getMLintern();
-    int getMLBase();
-    int getMLclosing();
-    int getTerminalAU();
-};
-}
-#endif