X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;h=110f019f3beeafdd2a877c423b250232a488e62c;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=d94cc95582f8d1482233a3cac0aee4b418dcc925;hpb=462fca6d24fd15ca035358ff70bcfae52c3281c3;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index d94cc95..110f019 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -33,17 +33,31 @@ 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 getOutputFileNameTag(string, string);
+	string getHelpString();	
+		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;
 		bool abort;
-		int seqLength;
+		int seqLength, haderror;
+		vector<string> outputNames;
+		map<string, int> nameMap;
 		
 		void readMap();
+		statData getStats(string sequence);
 };
 
 /**************************************************************************************************/