X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;fp=secondarystructurecommand.h;h=2e04936a8eea682d1f8511de11a16a601c9e9d1c;hb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;hp=0b654a4e02bdf42cdf5ebfc9ee419bdbd71eec2f;hpb=36a867cbd85d9c276d3c8d13f25a150bbbe2466b;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index 0b654a4..2e04936 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -35,20 +35,21 @@ 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();	
+	
+		int execute(); 
+		void help() { m->mothurOut(getHelpString()); }	
+	
 	private:
 		vector<int> structMap;
 		string mapfile, fastafile, outputDir, namefile;
 		bool abort;
 		int seqLength, haderror;
 		vector<string> outputNames;
-		map<string, vector<string> > outputTypes;
 		map<string, int> nameMap;
 		
 		void readMap();