X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterdoturcommand.cpp;h=5bcfe03416f90700a02a4ff3d58ad312f788bb96;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=b2b31edc27b9808ea9556e345d7d817429de1321;hpb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;p=mothur.git

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index b2b31ed..5bcfe03 100644
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -271,6 +271,25 @@ int ClusterDoturCommand::execute(){
 		//	m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine(); 
 		//}
 		
+		//set list file as new current listfile
+		string current = "";
+		itTypes = outputTypes.find("list");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+		}
+		
+		//set rabund file as new current rabundfile
+		itTypes = outputTypes.find("rabund");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+		}
+		
+		//set sabund file as new current sabundfile
+		itTypes = outputTypes.find("sabund");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
+		}
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}