X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.cpp;h=091bf9bb0659dd0895bf47a414fa4ea86692f026;hb=79a7d3273749b08d4f9f8dfe350c964ff0c4351e;hp=2f99aa6091452933f6796f21aa043449bfce1dd4;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index 2f99aa6..091bf9b 100644
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -46,7 +46,26 @@ string OtuHierarchyCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string OtuHierarchyCommand::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 == "otuheirarchy") {  outputFileName =  "otu.hierarchy"; }
+            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, "OtuHierarchyCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 OtuHierarchyCommand::OtuHierarchyCommand(){	
 	try {
@@ -180,7 +199,7 @@ int OtuHierarchyCommand::execute(){
 		}
 		
 		ofstream out;
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + "." + getOutputFileNameTag("otuheirarchy");
 		m->openOutputFile(outputFileName, out);
 		
 		//go through each bin in "big" otu and output the bins in "little" otu which created it
@@ -222,7 +241,7 @@ int OtuHierarchyCommand::execute(){
 		if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
 		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		m->mothurOut(outputFileName); m->mothurOutEndLine();	outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName); 
 		m->mothurOutEndLine();