X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=secondarystructurecommand.cpp;h=c2c104e71b1f535cd2a818afe268e5d7e1ed4c24;hb=648ec37228eb16075ace911dd5a5773cdfe683da;hp=7156082f8b1b43228a62c6cf93abec9f2d900109;hpb=5ca05ed0a8311b2943c1c0a1fad825785db484d6;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 7156082..c2c104e 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -91,11 +91,13 @@ int AlignCheckCommand::execute(){
 		
 		while(!in.eof()){
 			
-			Sequence seq(in);
-			statData data = getStats(seq.getAligned());
-			
-			out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
-			out << data.loop << '\t' << data.tilde << '\t' << data.total << endl;
+			Sequence seq(in);  gobble(in);
+			if (seq.getName() != "") {
+				statData data = getStats(seq.getAligned());
+				
+				out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
+				out << data.loop << '\t' << data.tilde << '\t' << data.total << endl;
+			}
 		}
 
 		in.close();