X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.h;h=f5493eb7517db72c20048da57080a587ae675f7e;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=b7fbf4342b821d1f6eb6dbb7094d94c3e85d19a3;hpb=f687723a8357916e86a05116978e6869b039ce36;p=mothur.git

diff --git a/trimflowscommand.h b/trimflowscommand.h
index b7fbf43..f5493eb 100644
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -26,8 +26,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "trim.flows";	}
 	string getCommandCategory()		{ return "Sequence Processing";		}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
 	string getDescription()		{ return "trim.flows"; }
 
@@ -223,7 +224,7 @@ static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
 				
 				flowData.printFlows(trimFlowFile);
 				
-				if(pDataArray->fasta)	{	currSeq.printSequence(fastaFile);	}
+				if(pDataArray->fasta)	{	currSeq.setAligned(currSeq.getUnaligned()); currSeq.printSequence(fastaFile);	}
 				
 				if(pDataArray->allFiles){
 					ofstream output;