/***********************************************************************/
//This is used by SharedJAbund and SharedSorAbund
-EstOutput SharedBrayCurtis::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
try {
- EstOutput data;
data.resize(1,0);
- int sumSharedA, sumSharedB, sumSharedAB, tempA, tempB;
+ double sumSharedA, sumSharedB, sumSharedAB, tempA, tempB;
sumSharedA = 0; sumSharedB = 0; sumSharedAB = 0;
/*Xi, Yi = abundance of the ith shared OTU in A and B
- sumSharedA = the sum of all shared otus in A
+ sumSharedA = the number of otus in A
sumSharedB = the sum of all shared otus in B
sumSharedAB = the sum of the minimum otus int all shared otus in AB.
*/
- for (int i = 0; i < shared1->size(); i++) {
+ for (int i = 0; i < shared[0]->size(); i++) {
//store in temps to avoid multiple repetitive function calls
- tempA = shared1->getAbundance(i);
- tempB = shared2->getAbundance(i);
-
+ tempA = shared[0]->getAbundance(i);
+ tempB = shared[1]->getAbundance(i);
- if ((tempA != 0) && (tempB != 0)) {//they are shared
- sumSharedA += tempA;
- sumSharedB += tempB;
+ sumSharedA += tempA;
+ sumSharedB += tempB;
- //sum the min of tempA and tempB
- if (tempA < tempB) { sumSharedAB += tempA; }
- else { sumSharedAB += tempB; }
- }
+ //sum the min of tempA and tempB
+ if (tempA < tempB) { sumSharedAB += tempA; }
+ else { sumSharedAB += tempB; }
}
data[0] = (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);
return data;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedBrayCurtis class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BrayCurtis", "getValues");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SharedBrayCurtis class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-
}
/***********************************************************************/