X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.cpp;h=dc40611711062150b7046e1be665a34c87d87818;hb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;hp=e23a0ac6a431ad14cdab21fb0bfa4276f4afd8c6;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index e23a0ac..dc40611 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -120,6 +120,7 @@ int AlignCheckCommand::execute(){
 
 		
 		while(!in.eof()){
+			if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
 			
 			Sequence seq(in);  gobble(in);
 			if (seq.getName() != "") {
@@ -135,6 +136,8 @@ int AlignCheckCommand::execute(){
 		in.close();
 		out.close();
 		
+		if (m->control_pressed) {  remove(outfile.c_str()); return 0; }
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 		m->mothurOut(outfile); m->mothurOutEndLine();