X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=secondarystructurecommand.h;h=ce97a2243c2b9da797e5a34da3454050b5002396;hp=daee85a37fd4e13df952ea363da36227dde85143;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index daee85a..ce97a22 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -39,15 +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;