X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.cpp;fp=phylotypecommand.cpp;h=c3aee4719859a4921ece77b25e7cf5dfe69d9aec;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=4b524dd09af79b7d9cc2653caec6eb9d4dfb36ad;hpb=5e031adc86a1fc125c4abb3d4048f209d52f9b6d;p=mothur.git

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 4b524dd..c3aee47 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -305,6 +305,25 @@ int PhylotypeCommand::execute(){
 			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();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}