X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitgroupscommand.cpp;fp=splitgroupscommand.cpp;h=16d90a48372f7c97d46f7fd4d0b640fde6b533fb;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=d389d8907bfaffde16b8ca9eac4dad0061341831;hpb=5e031adc86a1fc125c4abb3d4048f209d52f9b6d;p=mothur.git

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index d389d89..16d90a4 100644
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -184,6 +184,17 @@ int SplitGroupCommand::execute(){
 		
 		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0; }
 		
+		string current = "";
+		itTypes = outputTypes.find("fasta");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+		}
+		
+		itTypes = outputTypes.find("name");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+		}
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}