// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
-#include "GetCoreMicroBiomeCommand.h"
+#include "getcoremicrobiomecommand.h"
//**********************************************************************************************************************
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["coremicrobiom"] = tempOutNames;
+ outputTypes["coremicrobiome"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "GetCoreMicroBiomeCommand", "GetCoreMicroBiomeCommand");
}
}
-
+ vector<string> tempOutNames;
+ outputTypes["coremicrobiome"] = tempOutNames;
+
//check for parameters
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { abort = true; }
int GetCoreMicroBiomeCommand::createTable(vector<SharedRAbundFloatVector*>& lookup){
try {
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiom";
- outputNames.push_back(outputFileName); outputTypes["coremicrobiom"].push_back(outputFileName);
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiome";
+ outputNames.push_back(outputFileName); outputTypes["coremicrobiome"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
if (m->control_pressed) { return 0; }
if ((samples != -1) || (abund != -1)) {
- string outputFileName2 = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiomlist";
- outputNames.push_back(outputFileName2); outputTypes["coremicrobiom"].push_back(outputFileName2);
+ string outputFileName2 = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiomelist";
+ outputNames.push_back(outputFileName2); outputTypes["coremicrobiome"].push_back(outputFileName2);
ofstream out2;
m->openOutputFile(outputFileName2, out2);