/usr/include/libphylo/datMatrixHolder.h is in rate4site 3.0.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | // $Id: datMatrixHolder.h 5804 2009-01-20 09:18:05Z adido $
#ifndef ___DATMATRIXHOLDER
#define ___DATMATRIXHOLDER
#include <string>
using namespace std;
// THIS CONSTRUCT IS USED TO KEEP A STRING THAT IS THE AA SUBSTITUTION MATRIX
// THE datMatrixString IS TO BE USED WHENEVER WE USE ONE OF THE BUILD-IN AA SUBSTITUTION MATRICES.
class datMatrixString {
public:
const string Val;
explicit datMatrixString(const char * str): Val(str){};
};
class datMatrixHolder {
public:
static const datMatrixString cpREV45;
static const datMatrixString dayhoff;
static const datMatrixString jones; // This is JTT
static const datMatrixString mtREV24;
static const datMatrixString wag;
static const datMatrixString HIVb;
static const datMatrixString HIVw;
static const datMatrixString lg;
static const datMatrixString empiriCodon; //This is the empirical matrix for codon by gina and adrian
};
#endif // ___DATMATRIXHOLDER
|