exit(1);
}
}
-
//**********************************************************************************************************************
-
+string HomovaCommand::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 == "homova") { outputFileName = "homova"; }
+ 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, "HomovaCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
HomovaCommand::HomovaCommand(){
try {
abort = true; calledHelp = true;
string temp = validParameter.validFile(parameters, "iters", false);
if (temp == "not found") { temp = "1000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "alpha", false);
if (temp == "not found") { temp = "0.05"; }
- convert(temp, experimentwiseAlpha);
+ m->mothurConvert(temp, experimentwiseAlpha);
}
}
//create a new filename
ofstream HOMOVAFile;
- string HOMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + "homova";
+ string HOMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("homova");
m->openOutputFile(HOMOVAFileName, HOMOVAFile);
outputNames.push_back(HOMOVAFileName); outputTypes["homova"].push_back(HOMOVAFileName);