// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
-#include "GetCoreMicroBiomeCommand.h"
+#include "getcoremicrobiomecommand.h"
//**********************************************************************************************************************
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 {
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() + getOutputFileNameTag("coremicrobiome");
+ 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);