X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makebiomcommand.cpp;h=9e8d3e39cb58e31e9f3dca2eeff35257eadd537a;hb=5b72d1cf3fa48730e5bb70d59cced1e43e1fe424;hp=acd0500963d096acfb5d1ea453cc9186feafe783;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/makebiomcommand.cpp b/makebiomcommand.cpp
index acd0500..9e8d3e3 100644
--- a/makebiomcommand.cpp
+++ b/makebiomcommand.cpp
@@ -129,6 +129,27 @@ string MakeBiomCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string MakeBiomCommand::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 == "biom")             {   outputFileName =  "biom";       }
+            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, "MakeBiomCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+
 //**********************************************************************************************************************
 MakeBiomCommand::MakeBiomCommand(){	
 	try {
@@ -165,7 +186,7 @@ MakeBiomCommand::MakeBiomCommand(string option) {
 			for (it = parameters.begin(); it != parameters.end(); it++) { 
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
-			
+
 			//initialize outputTypes
 			vector<string> tempOutNames;
 			outputTypes["biom"] = tempOutNames;
@@ -352,7 +373,7 @@ int MakeBiomCommand::execute(){
 int MakeBiomCommand::getBiom(vector<SharedRAbundVector*>& lookup){
 	try {
         
-        string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + ".biom";
+        string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("biom");
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		outputNames.push_back(outputFileName); outputTypes["biom"].push_back(outputFileName);
@@ -612,7 +633,7 @@ vector<string> MakeBiomCommand::parseTax(string tax, vector<string>& scores) {
                         scores.push_back(confidenceScore);
 					}else{ scores.push_back("null"); }
 				}
-			}
+			}else{ scores.push_back("null"); }
 			
             //strip "" if they are there
             pos = taxon.find("\"");