//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
/***********************************************************/
int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
try {
/***********************************************************/
int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
try {
vector< vector< vector<seqDist> > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
vector< vector< vector<seqDist> > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
vector< vector<seqDist> > calcDists; calcDists.resize(matrixCalculators.size());
for (int thisIter = 0; thisIter < iters; thisIter++) {
vector< vector<seqDist> > calcDists; calcDists.resize(matrixCalculators.size());
for (int thisIter = 0; thisIter < iters; thisIter++) {