X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;h=c1cc057cd190cd4570b57d9bcc9f622a8f6bf0f4;hb=6a0001cc8c2f8de157f4979fd0d97a6e911b58e8;hp=dffb4cbd980ff504307465ae64a0f6645fe5e6a5;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index dffb4cb..c1cc057 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -33,7 +33,12 @@ 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();	
 		
@@ -41,7 +46,9 @@ class AlignCheckCommand : public Command {
 		vector<int> structMap;
 		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);