remove mafft extensions - we do not support them

[jabaws.git] / binaries / src / mafft / extensions / mxscarna_src / vienna / energy_par.h

diff --git a/binaries/src/mafft/extensions/mxscarna_src/vienna/energy_par.h b/binaries/src/mafft/extensions/mxscarna_src/vienna/energy_par.h
deleted file mode 100644 (file)
index 48b2737..0000000
--- a/binaries/src/mafft/extensions/mxscarna_src/vienna/energy_par.h
+++ /dev/null
@@ -1,61 +0,0 @@
-/* 
-   prototypes for energy_par.c
-*/
-
-#include "energy_const.h"
-namespace MXSCARNA {
-extern double lxc37;   /* parameter for logarithmic loop
-                         energy extrapolation            */
-
-extern int stack37[NBPAIRS+1][NBPAIRS+1];
-extern int enthalpies[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */
-extern int entropies[NBPAIRS+1][NBPAIRS+1];  /* not used anymore */
-
-extern int hairpin37[31];
-extern int bulge37[31];
-extern int internal_loop37[31];
-extern int internal2_energy;
-extern int old_mismatch_37[NBPAIRS+1][5][5];
-extern int mismatchI37[NBPAIRS+1][5][5];  /* interior loop mismatches */
-extern int mismatchH37[NBPAIRS+1][5][5];  /* same for hairpins */
-extern int mismatchM37[NBPAIRS+1][5][5];  /* same for multiloops */
-extern int mism_H[NBPAIRS+1][5][5];       /* mismatch enthalpies */
-
-extern int dangle5_37[NBPAIRS+1][5];      /* 5' dangle exterior of pair */
-extern int dangle3_37[NBPAIRS+1][5];      /* 3' dangle */
-extern int dangle3_H[NBPAIRS+1][5];       /* corresponding enthalpies */
-extern int dangle5_H[NBPAIRS+1][5];
-
-extern int int11_37[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */
-extern int int11_H[NBPAIRS+1][NBPAIRS+1][5][5];
-
-extern int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */
-extern int int21_H[NBPAIRS+1][NBPAIRS+1][5][5][5];
-
-extern int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */
-extern int int22_H[NBPAIRS+1][NBPAIRS+1][5][5][5][5];
-
-/* constants for linearly destabilizing contributions for multi-loops
-   F = ML_closing + ML_intern*(k-1) + ML_BASE*u  */
-extern int ML_BASE37;
-extern int ML_closing37;
-extern int ML_intern37;
-
-/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */
-/*    ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */
-extern int         MAX_NINIO;                   /* maximum correction */
-extern int F_ninio37[5];
-
-/* penalty for helices terminated by AU (actually not GC) */
-extern int TerminalAU;
-/* penalty for forming bi-molecular duplex */
-extern int DuplexInit;
-/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
-extern char Tetraloops[];  /* string containing the special tetraloops */
-extern int  TETRA_ENERGY37[];  /* Bonus energy for special tetraloops */
-extern int  TETRA_ENTH37;
-extern char Triloops[];    /* string containing the special triloops */
-extern int  Triloop_E37[]; /* Bonus energy for special Triloops */  
-
-extern double Tmeasure;       /* temperature of param measurements */
-}