int distance(sha1_hash *md1, sha1_hash *md2) {
int i;
int distance = 0;
for(i = 0; i < SHA_DIGEST_LENGTH; i++) {
distance += hamdist(md1[i], md2[i]);
}
return distance;
}
Data brute_force_viterbi_decoder(Message data) {
int min_dist = INT_MAX;
int dist;
Data best_fit;
int i;
for (i = 0; i < DATA_MAX; ++i) {
dist = hamdist(memory_falt_encoder(i), data);
if (dist < min_dist) {
min_dist = dist;
best_fit = i;
if (min_dist == 0) break;
}
}
return best_fit;
}
void distfun(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[], T classDummy)
{
int status;
mwSize numCoords,numPoints;
char metric[4];
T *x,*d,*arg,scalarArg;
/* get the metric */
status = mxGetString(prhs[1],metric,4);
/* create a pointer to the input matrix y */
x = (T*)mxGetData(prhs[0]);
/* get the dimensions of the matrix input y */
numCoords = mxGetM(prhs[0]);
numPoints = mxGetN(prhs[0]);
/* get extra arg */
if (nrhs>2 && !mxIsEmpty(prhs[2])) {
if (mxGetNumberOfElements(prhs[2]) == 1) { /*scalar case */
scalarArg = (T)mxGetScalar(prhs[2]);
} else if (mxGetClassID(prhs[2]) == mxGetClassID(prhs[0])) {
arg = (T*)mxGetData(prhs[2]);
} else {
mexErrMsgIdAndTxt("stats:pdistmex:MixedInputTypes",
"Additional input arguments must be the same class as X.");
}
}
/* make sure that the distance matrix can be created, then create it. doing
* this in double remains exact except in the cases where we error out anyway. */
double numDists = ((double)numPoints * (double)(numPoints-1)) / 2;
if (numDists >= (double)MWSIZE_MAX) {
mexErrMsgIdAndTxt("stats:pdistmex:OutputTooLarge",
"Distance matrix has more elements than the maximum allowed size in MATLAB.");
}
plhs[0] = mxCreateNumericMatrix(1, (mwSize)numDists, mxGetClassID(prhs[0]), mxREAL);
/* create a pointer to a copy of the output matrix */
d = (T*)mxGetData(plhs[0]);
/* call the appropriate distance subroutine */
if (strcmp(metric,"euc") == 0)
eucdist(x,numPoints,numCoords,d);
else if(strcmp(metric,"seu") == 0)
seudist(x,numPoints,numCoords,arg,d);
else if(strcmp(metric,"cit") == 0)
citdist(x,numPoints,numCoords,d);
else if(strcmp(metric,"min") == 0)
mindist(x,numPoints,numCoords,scalarArg,d);
else if(strcmp(metric,"cos") == 0)
coscordist(x,numPoints,numCoords,d);
else if(strcmp(metric,"cor") == 0)
coscordist(x,numPoints,numCoords,d);
else if(strcmp(metric,"spe") == 0)
coscordist(x,numPoints,numCoords,d);
else if(strcmp(metric,"ham") == 0)
hamdist(x,numPoints,numCoords,d);
else if(strcmp(metric,"jac") == 0)
jacdist(x,numPoints,numCoords,d);
else if(strcmp(metric,"che") == 0)
chedist(x,numPoints,numCoords,d);
else if(strcmp(metric,"mah") == 0)
mahdist(x,numPoints,numCoords,arg,d);
}
unsigned hamdist(const ExpandedKMer &k,
unsigned tau = hammer::K) const {
return hamdist(k.s_, tau);
}
