exit(1);
}
}
+//**********************************************************************************************************************
+string GetCoreMicroBiomeCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "coremicrobiome") { outputFileName = "core.microbiome"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCoreMicroBiomeCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(){
try {
int GetCoreMicroBiomeCommand::createTable(vector<SharedRAbundFloatVector*>& lookup){
try {
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiome";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + getOutputFileNameTag("coremicrobiome");
outputNames.push_back(outputFileName); outputTypes["coremicrobiome"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);