X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clusterdoturcommand.cpp;h=9bfb52b9d92b0222af2e4b1acff37c82f968349f;hp=603bd73d680b485fb4df6ef6cf62e935af3f1ff5;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hpb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 603bd73..9bfb52b 100644
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -49,6 +49,28 @@ string ClusterDoturCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ClusterDoturCommand::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 == "list") {  outputFileName =  "list"; }
+            else if (type == "rabund") {  outputFileName =  "rabund"; }
+            else if (type == "sabund") {  outputFileName =  "sabund"; }
+            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, "ClusterDoturCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 ClusterDoturCommand::ClusterDoturCommand(){	
 	try {
 		abort = true; calledHelp = true;
@@ -201,13 +223,17 @@ int ClusterDoturCommand::execute(){
 		if (outputDir == "") { outputDir += m->hasPath(phylipfile); }
 		fileroot = outputDir + m->getRootName(m->getSimpleName(phylipfile));
 			
-		m->openOutputFile(fileroot+ tag + ".sabund",	sabundFile);
-		m->openOutputFile(fileroot+ tag + ".rabund",	rabundFile);
-		m->openOutputFile(fileroot+ tag + ".list",		listFile);
-				
-		outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
-		outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
-		outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
+        string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
+        string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
+        string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+        
+		m->openOutputFile(sabundFileName,	sabundFile);
+		m->openOutputFile(rabundFileName,	rabundFile);
+		m->openOutputFile(listFileName,	listFile);
+		
+		outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+		outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+		outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
 		
 		float previousDist = 0.00000;
 		float rndPreviousDist = 0.00000;