X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;h=0b654a4e02bdf42cdf5ebfc9ee419bdbd71eec2f;hb=4f9a6e14a608172f8a97f0297a3b8e6ea267c518;hp=c1cc057cd190cd4570b57d9bcc9f622a8f6bf0f4;hpb=32abf5d58aed8087cd0bcb32d7aa9053f103f2c1;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index c1cc057..0b654a4 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -44,11 +44,12 @@ class AlignCheckCommand : public Command {
 		
 	private:
 		vector<int> structMap;
-		string mapfile, fastafile, outputDir;
+		string mapfile, fastafile, outputDir, namefile;
 		bool abort;
 		int seqLength, haderror;
 		vector<string> outputNames;
 		map<string, vector<string> > outputTypes;
+		map<string, int> nameMap;
 		
 		void readMap();
 		statData getStats(string sequence);