//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 (inputDir == "not found"){ inputDir = ""; }
//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 (inputDir == "not found"){ inputDir = ""; }
if (format == "sharedfile") {
//if the users entered no valid calculators don't execute command
if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
if (format == "sharedfile") {
//if the users entered no valid calculators don't execute command
if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
//create treemap class from groupmap for tree class to use
tmap = new TreeMap();
tmap->makeSim(globaldata->gGroupmap);
globaldata->gTreemap = tmap;
//create treemap class from groupmap for tree class to use
tmap = new TreeMap();
tmap->makeSim(globaldata->gGroupmap);
globaldata->gTreemap = tmap;
subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
data = treeCalculators[i]->getValues(subset); //saves the calculator outputs