X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=hclustercommand.cpp;h=128dee379080ddf32704367789c916d3bce14f41;hp=94082dfc74dfe0969e769572fc6df219ecaa69d2;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hpb=5e031adc86a1fc125c4abb3d4048f209d52f9b6d

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index 94082df..128dee3 100644
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -395,7 +395,26 @@ int HClusterCommand::execute(){
 			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
 			return 0;  
 		}
-
+		
+		//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();