X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=secondarystructurecommand.h;h=ce97a2243c2b9da797e5a34da3454050b5002396;hp=2e04936a8eea682d1f8511de11a16a601c9e9d1c;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index 2e04936..ce97a22 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -39,14 +39,19 @@ class AlignCheckCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "align.check";				}
 		string getCommandCategory()		{ return "Sequence Processing";		}
-		string getHelpString();	
+		
+	string getHelpString();	
+    string getOutputPattern(string);	
+		string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
+		string getDescription()		{ return "calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment"; }
+
 	
 		int execute(); 
 		void help() { m->mothurOut(getHelpString()); }	
 	
 	private:
 		vector<int> structMap;
-		string mapfile, fastafile, outputDir, namefile;
+		string mapfile, fastafile, outputDir, namefile, countfile;
 		bool abort;
 		int seqLength, haderror;
 		vector<string> outputNames;