X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;fp=secondarystructurecommand.h;h=c1cc057cd190cd4570b57d9bcc9f622a8f6bf0f4;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hp=2e6191ca67f47f92f38bb8c030a8ad3e32920af6;hpb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index 2e6191c..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();	
 		
@@ -42,6 +47,8 @@ class AlignCheckCommand : public Command {
 		string mapfile, fastafile, outputDir;
 		bool abort;
 		int seqLength, haderror;
+		vector<string> outputNames;
+		map<string, vector<string> > outputTypes;
 		
 		void readMap();
 		statData getStats(string sequence);