X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;h=ce97a2243c2b9da797e5a34da3454050b5002396;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=a82cf4e5edd89a5536cfbecafb5def8f6a7e3ed4;hpb=cc1838f288a7712d44929fca5175ce89f3a58f12;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index a82cf4e..ce97a22 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -33,15 +33,29 @@ class AlignCheckCommand : public Command {
 	public:
 	
 		AlignCheckCommand(string);	
-		~AlignCheckCommand(){};
-		int execute();
-		void help();	
+		AlignCheckCommand();
+		~AlignCheckCommand(){}
+	
+		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;
+		string mapfile, fastafile, outputDir, namefile, countfile;
 		bool abort;
-		int seqLength;
+		int seqLength, haderror;
+		vector<string> outputNames;
+		map<string, int> nameMap;
 		
 		void readMap();
 		statData getStats(string sequence);