if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
else { inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
-
+
for (int p = 0; p < inputFileNames.size(); p++) {
-
+
if (outputDir == "") { outputDir += hasPath(inputFileNames[p]); }
string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
globaldata->inputFileName = inputFileNames[p];
-
+
if (inputFileNames.size() > 1) {
mothurOutEndLine(); mothurOut("Processing group " + groups[p]); mothurOutEndLine(); mothurOutEndLine();
}
-
+
validCalculator = new ValidCalculators();
for (int i=0; i<Estimators.size(); i++) {
}
}
-
//if the users entered no valid calculators don't execute command
if (cDisplays.size() == 0) { return 0; }
read = new ReadOTUFile(inputFileNames[p]);
read->read(&*globaldata);
-
+
order = globaldata->gorder;
string lastLabel = order->getLabel();
input = globaldata->ginput;