X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;fp=secondarystructurecommand.h;h=dffb4cbd980ff504307465ae64a0f6645fe5e6a5;hb=315e38cf393c82be238da5b32574f225a020d25c;hp=a82cf4e5edd89a5536cfbecafb5def8f6a7e3ed4;hpb=c99f3846e7a7b6f06ab46508baa5409204ad6290;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index a82cf4e..dffb4cb 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -39,7 +39,7 @@ class AlignCheckCommand : public Command {
 		
 	private:
 		vector<int> structMap;
-		string mapfile, fastafile;
+		string mapfile, fastafile, outputDir;
 		bool abort;
 		int seqLength;