9 files changed, 1240 insertions, 0 deletions
diff --git a/test/entropy/FastNWalign2.c b/test/entropy/FastNWalign2.c
new file mode 100644
index 0000000..33b286d
--- a/dev/null
+++ b/test/entropy/FastNWalign2.c
@@ -0,0 +1,94 @@
+#include "mex.h"
+#include "matrix.h"
+void simplegap(double scoredMatchMat[],
+const double gap, int n, int m, double output_F[], double output_P[])
+{
+    // Standard Needleman-Wunsch algorithm
+    
+    double up, left, diagonal, best, pos;
+    
+    
+    int i,j;
+    
+    for(i=0;i<m;i++)
+    {
+        output_F[i]=i*gap;
+        output_P[i]=2;
+    }
+    
+    
+    for(j=0; j<n; j++)  //put initial values in
+    {
+        output_F[j*m]=j*gap;
+        output_P[j*m]=4;
+    }
+    output_P[0]=1;
+    
+   
+    for(j=1;j<n;j++) //cycle through columns
+    {
+         best=output_F[(j)*m];
+         for(i=1; i<m; i++) //cycle through the rows
+         {
+             up=best+gap;
+             left=output_F[i+(j-1)*m]+gap;
+             diagonal=output_F[i-1+(j-1)*m]+scoredMatchMat[i-1+(j-1)*m];
+             
+             if (up>left)
+             {
+                 best=up;
+                 pos=2;
+             }
+             else
+            {
+                best=left;
+                pos=4;
+            }
+            
+            if (diagonal>=best)
+            {
+                best=diagonal;
+                output_P[i+j*m]=1;
+            }
+            else
+            {
+                output_P[i+j*m]=pos;
+            }
+            output_F[i+j*m]=best;
+        }
+    }
+}
+void mexFunction(int nlhs, mxArray *plhs[],
+int nrhs, const mxArray *prhs[])
+{
+    
+    double *gap, *output_F, *output_P;
+    double *scoredMatchMat;
+    int n, m;
+    mwSize i;
+    
+    //double *F_col, *ptr_col;
+    m=mxGetM(prhs[0]);
+    n=mxGetN(prhs[0]);
+    gap=mxGetPr(prhs[1]);
+    
+    plhs[0]=mxCreateDoubleMatrix(m,n,mxREAL);
+    plhs[1]=mxCreateDoubleMatrix(m,n,mxREAL);
+    
+    output_F=mxGetPr(plhs[0]);
+    output_P=mxGetPr(plhs[1]);
+    
+    
+    scoredMatchMat=mxGetPr(prhs[0]);
+    //
+    
+    
+    simplegap(scoredMatchMat,*gap,n,m,output_F,output_P);
+    
+}

diff --git a/test/entropy/FastNWalign2.c b/test/entropy/FastNWalign2.c new file mode 100644 index 0000000..33b286d --- a/dev/null +++ b/test/entropy/FastNWalign2.c
@@ -0,0 +1,94 @@
	1	#include "mex.h"
	2	#include "matrix.h"
	3
	4	void simplegap(double scoredMatchMat[],
	5	const double gap, int n, int m, double output_F[], double output_P[])
	6	{
	7	// Standard Needleman-Wunsch algorithm
	8
	9	double up, left, diagonal, best, pos;
	10
	11
	12	int i,j;
	13
	14
	15	for(i=0;i<m;i++)
	16	{
	17	output_F[i]=i*gap;
	18	output_P[i]=2;
	19	}
	20
	21
	22	for(j=0; j<n; j++) //put initial values in
	23	{
	24	output_F[jm]=jgap;
	25	output_P[j*m]=4;
	26	}
	27	output_P[0]=1;
	28
	29
	30
	31	for(j=1;j<n;j++) //cycle through columns
	32	{
	33	best=output_F[(j)*m];
	34
	35	for(i=1; i<m; i++) //cycle through the rows
	36	{
	37	up=best+gap;
	38	left=output_F[i+(j-1)*m]+gap;
	39	diagonal=output_F[i-1+(j-1)m]+scoredMatchMat[i-1+(j-1)m];
	40
	41	if (up>left)
	42	{
	43	best=up;
	44	pos=2;
	45	}
	46	else
	47	{
	48	best=left;
	49	pos=4;
	50	}
	51
	52	if (diagonal>=best)
	53	{
	54	best=diagonal;
	55	output_P[i+j*m]=1;
	56	}
	57	else
	58	{
	59	output_P[i+j*m]=pos;
	60	}
	61	output_F[i+j*m]=best;
	62	}
	63	}
	64	}
	65
	66	void mexFunction(int nlhs, mxArray *plhs[],
	67	int nrhs, const mxArray *prhs[])
	68	{
	69
	70	double gap, output_F, *output_P;
	71	double *scoredMatchMat;
	72	int n, m;
	73	mwSize i;
	74
	75	//double F_col, ptr_col;
	76	m=mxGetM(prhs[0]);
	77	n=mxGetN(prhs[0]);
	78	gap=mxGetPr(prhs[1]);
	79
	80	plhs[0]=mxCreateDoubleMatrix(m,n,mxREAL);
	81	plhs[1]=mxCreateDoubleMatrix(m,n,mxREAL);
	82
	83	output_F=mxGetPr(plhs[0]);
	84	output_P=mxGetPr(plhs[1]);
	85
	86
	87	scoredMatchMat=mxGetPr(prhs[0]);
	88	//
	89
	90
	91	simplegap(scoredMatchMat,*gap,n,m,output_F,output_P);
	92
	93	}
	94