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#include <iostream>
#include <cmath>
#include <string>
#include <algorithm>
#include <lua.h>
using namespace std;
// Find the directory to the lua root and substitute for C:\lua
//g++ --shared -I"C:\lua\include" nw.cpp "C:\lua\lib\lua51.lib" -o nw.dll
enum NW_PENALTIES{
MATCH = 1,
NOMATCH = -1,
GAP = -1
};
enum NW_DIR{
mch,
hrz,
vrt
};
int match(char a, char b){
return (a==b) ? MATCH : NOMATCH;
}
int* select(int o, int top, int left){
int* _ret = (int*)malloc(2*sizeof(int));
_ret[0] = hrz;_ret[1] = left;
if (o>= top && o>= left){
_ret[0] = mch;_ret[1] = o;
return _ret;
}else if (top >= left){
_ret[0] = vrt;_ret[1] = top;
return _ret;
}
return _ret;
}
int*** makeMatrix(string A, string B){
int a = A.length()+1, b = B.length()+1;
int*** _matrix = (int***)malloc(a*sizeof(int));
for (int i=0;i<a;i++){
_matrix[i] = (int**)malloc(b*sizeof(int));
for (int j=0;j<b;j++){
_matrix[i][j] = (int*)malloc(2*sizeof(int));
if (i == 0)
_matrix[i][j][0] = hrz,
_matrix[i][j][1] = j*NOMATCH;
else if (j == 0)
_matrix[i][j][0] = vrt,
_matrix[i][j][1] = i*NOMATCH;
else
_matrix[i][j][0] = 0,
_matrix[i][j][1] = 0;
}
}
for (int i=1;i<a;i++){
for (int j = 1; j<b; j++){
int m, v, h;
// m = i-1, j-1
// v = i-1, j
// h = i, j-1
m = (_matrix)[i-1][j-1][1] + match(A[i-1],B[j-1]);
v = (_matrix)[i-1][j][1] + GAP;
h = (_matrix)[i][j-1][1] + GAP;
_matrix[i][j] = select(m,v,h);
}
}
return _matrix;
}
int numtrace(int*** _matrix, string A, string B){
int i__ = A.length(), j__ = B.length();
int n = 0;
while (i__>0 && j__ >0){
int dir = _matrix[i__][j__][0];
switch(dir){
case 0:
i__--;j__--;
break;
case 1:
j__--;
break;
case 2:
i__--;
break;
}
n++;
}
return n+max(i__,j__);
}
int trace(int*** _matrix, string A, string B, int* num){
int n = numtrace(_matrix, A, B);
*num = n;
int i = A.length(), j = B.length();
int mutations = 0;
while (i>0 || j >0){
int dir = _matrix[i][j][0];
switch(dir){
case 0:
if (A[i-1] != B[j-1]) mutations++;
i--;j--;
break;
case 1:
j--;
mutations++;
break;
case 2:
i--;
mutations++;
break;
}
n--;
}
return mutations;
}
char** trace_align(int*** _matrix, string A, string B){
char** sequences = (char**)malloc(2*sizeof(char));
int n = numtrace(_matrix, A, B);
sequences[1] = (char*)malloc(n*sizeof(char)); // +1 to allocate for string type
sequences[0] = (char*)malloc(n*sizeof(char));
int i = A.length(), j = B.length();
int mutations = 0;
while (i>0 || j >0){
int dir = _matrix[i][j][0];
cout << dir << " " << n << "\n";
switch(dir){
case 0:
// back both ways
//cout << i << " , " << j << "\t" << A[i-1] << " " << B[j-1] << endl;
sequences[1][n-1] = A[i-1];
sequences[0][n-1] = B[j-1];
if (A[i-1] != B[j-1]) mutations++;
i--;j--;
break;
case 1:
// left
//cout << i << " , " << j << "\t" << "-" << " " << B[j-1] << endl;
sequences[1][n-1] = '-';
sequences[0][n-1] = B[j-1];
j--;
mutations++;
break;
case 2:
// up
//cout << i << " , " << j << "\t" << A[i-1] << " " << "-" << endl;
sequences[1][n-1] = A[i-1];
sequences[0][n-1] = '-';
i--;
mutations++;
break;
}
n--;
}
return sequences;
}
int mutate_(string A, string B, int* n){
int*** matrix = makeMatrix(A,B);
int seqs = trace(matrix,A,B, n);
return seqs;
}
char** align_(string A, string B){
int*** matrix = makeMatrix(A,B);
char** seqs = trace_align(matrix,A,B);
return seqs;
}
static int l_align(lua_State *l){
char** align = align(luaL_checkstring(l, 1), luaL_checkstring(l, 2));
lua_pushstring(align[0]);
lua_pushstring(align[1]);
return 2;
}
static int l_mutate(lua_State *l){
int n = 0;
int mutations = mutate_(luaL_checkstring(l, 1), luaL_checkstring(l, 2), &n);
lua_pushinteger(l, mutations);
lua_pushinteger(l, n);
return 2
}
static const luaL_Reg new_reg[] =
{
{ "align", l_align},
{ "percent_difference", l_mutate},
{ NULL, NULL }
};
LUALIB_API int luaopen_nw(lua_State *l){
luaL_register(l,"nw",nw_reg);
return 1;
}
CS2D 
return string diffrence in %
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