X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;h=ce97a2243c2b9da797e5a34da3454050b5002396;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=4e7bdea09cac0d1bd86d780eb92e499bbe9bfc69;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index 4e7bdea..ce97a22 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -39,7 +39,9 @@ class AlignCheckCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "align.check";				}
 		string getCommandCategory()		{ return "Sequence Processing";		}
-		string getHelpString();	
+		
+	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"; }
 
@@ -49,7 +51,7 @@ class AlignCheckCommand : public Command {
 	
 	private:
 		vector<int> structMap;
-		string mapfile, fastafile, outputDir, namefile;
+		string mapfile, fastafile, outputDir, namefile, countfile;
 		bool abort;
 		int seqLength, haderror;
 		vector<string> outputNames;