X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;h=c1cc057cd190cd4570b57d9bcc9f622a8f6bf0f4;hb=d9b668f68b99f92ecdc71dd8cd363cb4e27107f9;hp=d94cc95582f8d1482233a3cac0aee4b418dcc925;hpb=462fca6d24fd15ca035358ff70bcfae52c3281c3;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index d94cc95..c1cc057 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -33,17 +33,25 @@ class AlignCheckCommand : public Command {
 	public:
 	
 		AlignCheckCommand(string);	
-		~AlignCheckCommand(){};
+		AlignCheckCommand();
+		~AlignCheckCommand(){}
+		vector<string> getRequiredParameters();
+		vector<string> getValidParameters();
+		vector<string> getRequiredFiles();
+		map<string, vector<string> > getOutputFiles() { return outputTypes; }
 		int execute();
 		void help();	
 		
 	private:
 		vector<int> structMap;
-		string mapfile, fastafile;
+		string mapfile, fastafile, outputDir;
 		bool abort;
-		int seqLength;
+		int seqLength, haderror;
+		vector<string> outputNames;
+		map<string, vector<string> > outputTypes;
 		
 		void readMap();
+		statData getStats(string sequence);
 };
 
 /**************************************************************************************************/