Removing old version of mafft to replace with the new

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

diff --git a/binaries/src/mafft/extensions/mxscarna_src/Util.hpp b/binaries/src/mafft/extensions/mxscarna_src/Util.hpp
deleted file mode 100644 (file)
index eab7667..0000000
--- a/binaries/src/mafft/extensions/mxscarna_src/Util.hpp
+++ /dev/null
@@ -1,102 +0,0 @@
-#ifndef UTIL_H
-#define UTIL_H
-
-#include <algorithm>
-#include <cassert>
-#include <cstdio>
-#include <cstdlib>
-#include <cstdarg>
-#include <cstring>
-#include <cmath>
-#include <cctype>
-#include <climits>
-#include <cfloat>
-#include <ctime>
-#include <fstream>
-#include <functional>
-#include <iomanip>
-#include <iostream>
-#include <iterator>
-#include <list>
-#include <map>
-#include <numeric>
-#include <string>
-#include <sstream>
-#include <stack>
-#include <vector>
-#include <fcntl.h>
-#include <unistd.h>
-//#include <pthread.h> // mingw de error, by katoh
-#include <signal.h>
-
-namespace ProbCons {
-    
-const double IMPOSSIBLE = -FLT_MAX + 1000;
-const double IMPOSSIBLEDBL = -DBL_MAX + 10000;
-
-namespace MXSCARNA {
-template <typename T>
-inline bool
-IsPossible(const T& v) { 
-    return (v > (IMPOSSIBLE + 1.0e-5));
-}
-
-template <typename T>
-inline T
-logSum(const T& a, const T& b)
-{
-    if (a >= b) {
-       return a + log(1.0 + exp(b - a));
-    } else {
-       return b + log(1.0 + exp(a - b));
-    }
-}
-
-template <typename T>
-inline T
-logSub(const T&a, const T& b)
-{
-  if(a > b) {
-    return log(exp(a) - exp(b));
-  }
-  else {
-    return log(exp(a) - exp(b));
-  }
-}
-
-template <typename T>
-inline T
-logSum(const T& a, const T& b, const T& c)
-{
-    if (a >= b) {
-       if( a >= c ) {
-           return a + log(1.0 + (exp(b - a) + exp(c - a)));
-       }
-       else {
-           if( b >= c) {
-               return b + log(exp(a - b) + 1.0 + exp(c - b));
-           }
-       }
-    }
-    return c + log(exp(a - c) + exp(b - c) + 1.0);
-}
-
-}
-
-template <typename T>
-inline T
-logSumExp(const T& x, const T& y)
-{
-    if(x == y) return x + 0.69314718055;
-    double vmin = std::min(x, y);
-    double vmax = std::max(x, y);
-    
-    if (vmax > vmin + 50) {
-       return vmax;
-    }
-    else {
-       return vmax + std::log (std::exp (vmin - vmax) + 1.0);
-    }
-}
-}
-#endif /* UTIL_H */