+
+//int AmovaCommand::process(vector<SharedRAbundVector*> thisLookup) {
+// try{
+//
+//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+// if(processors == 1){
+// driver(0, namesOfGroupCombos.size(), thisLookup, "");
+// }else{
+// int process = 1;
+// vector<int> processIDS;
+//
+// //loop through and create all the processes you want
+// while (process != processors) {
+// int pid = fork();
+//
+// if (pid > 0) {
+// processIDS.push_back(pid);
+// process++;
+// }else if (pid == 0){
+// driver(lines[process].start, lines[process].num, thisLookup, toString(getpid()));
+// exit(0);
+// }else {
+// m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+// for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+// exit(0);
+// }
+// }
+//
+// //do my part
+// driver(lines[0].start, lines[0].num, thisLookup, "");
+//
+// //force parent to wait until all the processes are done
+// for (int i=0;i<(processors-1);i++) {
+// int temp = processIDS[i];
+// wait(&temp);
+// }
+//
+// //append files
+// for(int i = 0 ; i < calculators.size(); i++) {
+// string outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + calculators[i]->getName() + ".amova";
+//
+// for (int j = 0; j < processIDS.size(); j++) {
+// m->appendFiles((outputFile + toString(processIDS[j])), outputFile);
+// remove((outputFile + toString(processIDS[j])).c_str());
+// }
+// }
+// }
+//#else
+// driver(0, namesOfGroupCombos.size(), thisLookUp, "");
+//#endif
+//
+// return 0;
+// }
+// catch(exception& e) {
+// m->errorOut(e, "AmovaCommand", "process");
+// exit(1);
+// }
+//}
+
+//**********************************************************************************************************************
+
+//int AmovaCommand::driver(int start, int num, vector<SharedRAbundVector*> thisLookup, string pidValue) {
+// try {
+// vector<SharedRAbundVector*> subset;
+// EstOutput data;
+//
+// //for each calculator
+// for(int i = 0 ; i < calculators.size(); i++) {
+//
+// //create a new filename
+// ofstream out;
+// string outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + calculators[i]->getName() + ".amova" + pidValue;
+// m->openOutputFileAppend(outputFile, out);
+// out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+//
+// //for each combo
+// for (int c = start; c < (start+num); c++) {
+//
+// if (m->control_pressed) { out.close(); return 0; }
+//
+// //get set names
+// vector<string> setNames;
+// for (int j = 0; j < namesOfGroupCombos[c].size(); j++) { setNames.push_back(namesOfGroupCombos[c][j]); }
+//
+// vector<SharedRAbundVector*> thisCombosLookup;
+// vector<string> thisCombosLookupSets; //what set each sharedRabund is from to be used when calculating SSWithin
+// for (int k = 0; k < thisLookup.size(); k++) {
+// string thisGroup = thisLookup[k]->getGroup();
+//
+// //is this group for a set we want to compare??
+// if (m->inUsersGroups(designMap->getGroup(thisGroup), setNames)) {
+// thisCombosLookup.push_back(thisLookup[k]);
+// thisCombosLookupSets.push_back(designMap->getGroup(thisGroup));
+// }
+//
+// }
+//
+// int numGroups = thisCombosLookup.size();
+//
+// //calc the distance matrix
+// matrix.clear();
+// matrix.resize(numGroups);
+// for (int k = 0; k < matrix.size(); k++) { for (int j = 0; j < matrix.size(); j++) { matrix[k].push_back(1.0); } }
+//
+// if (thisCombosLookup.size() == 0) {
+// m->mothurOut("[ERROR]: Missing shared info for sets. Skipping comparison."); m->mothurOutEndLine();
+// }else{
+//
+// m->mothurOut(thisLookup[0]->getLabel() + '\t');
+// out << thisLookup[0]->getLabel() << '\t';
+// if (setNames.size() == 2) {
+// m->mothurOut(setNames[0] + '-' + setNames[1] + '\t');
+// out << setNames[0] << "-" << setNames[1] << '\t';
+// }
+// else {
+// out << "all" << '\t';
+// m->mothurOut("all\t");
+// }
+//
+// for (int k = 0; k < thisCombosLookup.size(); k++) {
+// for (int l = k; l < thisCombosLookup.size(); l++) {
+//
+// if (m->control_pressed) { out.close(); return 0; }
+//
+// if (k != l) { //we dont need to similiarity of a groups to itself
+// //get estimated similarity between 2 groups
+// subset.clear(); //clear out old pair of sharedrabunds
+// //add new pair of sharedrabunds
+// subset.push_back(thisCombosLookup[k]); subset.push_back(thisCombosLookup[l]);
+//
+// //if this calc needs all groups to calculate the pair load all groups
+// if (calculators[i]->getNeedsAll()) {
+// //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+// for (int w = 0; w < thisCombosLookup.size(); w++) {
+// if ((w != k) && (w != l)) { subset.push_back(thisCombosLookup[w]); }
+// }
+// }
+//
+// data = calculators[i]->getValues(subset); //saves the calculator outputs
+//
+// //save values in similarity matrix
+// matrix[k][l] = 1.0 - data[0];
+// matrix[l][k] = 1.0 - data[0];
+// }
+// }
+// }
+//
+// //calc amova
+// calcAmova(out, setNames.size(), thisCombosLookupSets);
+// }
+// }
+//
+// out.close();
+// }
+//
+// return 0;
+//
+// }
+// catch(exception& e) {
+// m->errorOut(e, "AmovaCommand", "driver");
+// exit(1);
+// }
+//}
+//
+//**********************************************************************************************************************
+//
+//int AmovaCommand::driver(int start, int num, vector<string> names, string pidValue, vector< vector<double> >& completeMatrix) {
+// try {
+//
+// //create a new filename
+// ofstream out;
+// string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipFile)) + "amova" + pidValue;
+// m->openOutputFileAppend(outputFile, out);
+// out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+//
+// //for each combo
+// for (int c = start; c < (start+num); c++) {
+//
+// if (m->control_pressed) { out.close(); return 0; }
+//
+// //get set names
+// vector<string> setNames;
+// for (int j = 0; j < namesOfGroupCombos[c].size(); j++) { setNames.push_back(namesOfGroupCombos[c][j]); }
+//
+// vector<string> thisCombosSets; //what set each line in the distance matrix is from to be used when calculating SSWithin
+// set<int> indexes;
+// for (int k = 0; k < names.size(); k++) {
+// //is this group for a set we want to compare??
+// if (m->inUsersGroups(designMap->getGroup(names[k]), setNames)) {
+// thisCombosSets.push_back(designMap->getGroup(names[k]));
+// indexes.insert(k); //save indexes of valid rows in matrix for submatrix
+// }
+// }
+//
+// int numGroups = thisCombosSets.size();
+//
+// //calc the distance matrix
+// matrix.clear();
+// matrix.resize(numGroups);
+//
+// for (int k = 0; k < matrix.size(); k++) { for (int j = 0; j < matrix.size(); j++) { matrix[k].push_back(1.0); } }
+//
+// if (thisCombosSets.size() == 0) {
+// m->mothurOut("[ERROR]: Missing distance info for sets. Skipping comparison."); m->mothurOutEndLine();
+// }else{
+//
+// if (setNames.size() == 2) {
+// out << setNames[0] << "-" << setNames[1] << '\t';
+// m->mothurOut(setNames[0] + '-' + setNames[1] + '\t');
+// }
+// else {
+// out << "all" << '\t';
+// m->mothurOut("all\t");
+// }
+//
+// //fill submatrix
+// int rowCount = 0;
+// for (int j = 0; j < completeMatrix.size(); j++) {
+//
+// if (indexes.count(j) != 0) { //we want at least part of this row
+// int columnCount = 0;
+// for (int k = 0; k < completeMatrix[j].size(); k++) {
+//
+// if (indexes.count(k) != 0) { //we want this distance
+// matrix[rowCount][columnCount] = completeMatrix[j][k];
+// matrix[columnCount][rowCount] = completeMatrix[j][k];
+// columnCount++;
+// }
+// }
+// rowCount++;
+// }
+// }
+//
+// //calc amova
+// calcAmova(out, setNames.size(), thisCombosSets);
+// }
+// }
+//
+// out.close();
+//
+//
+// return 0;
+//
+// }
+// catch(exception& e) {
+// m->errorOut(e, "AmovaCommand", "driver");
+// exit(1);
+// }
+//}
+//