X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=secondarystructurecommand.h;h=ce97a2243c2b9da797e5a34da3454050b5002396;hp=0b654a4e02bdf42cdf5ebfc9ee419bdbd71eec2f;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=4f9a6e14a608172f8a97f0297a3b8e6ea267c518

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index 0b654a4..ce97a22 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -35,20 +35,26 @@ class AlignCheckCommand : public Command {
 		AlignCheckCommand(string);	
 		AlignCheckCommand();
 		~AlignCheckCommand(){}
-		vector<string> getRequiredParameters();
-		vector<string> getValidParameters();
-		vector<string> getRequiredFiles();
-		map<string, vector<string> > getOutputFiles() { return outputTypes; }
-		int execute();
-		void help();	
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "align.check";				}
+		string getCommandCategory()		{ return "Sequence Processing";		}
 		
+	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;
-		map<string, vector<string> > outputTypes;
 		map<string, int> nameMap;
 		
 		void readMap();