X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;h=ce97a2243c2b9da797e5a34da3454050b5002396;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=c1cc057cd190cd4570b57d9bcc9f622a8f6bf0f4;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index c1cc057..ce97a22 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -35,20 +35,27 @@ 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();	
+    string getOutputPattern(string);	
+		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, outputDir;
+		string mapfile, fastafile, outputDir, namefile, countfile;
 		bool abort;
 		int seqLength, haderror;
 		vector<string> outputNames;
-		map<string, vector<string> > outputTypes;
+		map<string, int> nameMap;
 		
 		void readMap();
 		statData getStats(string sequence);