X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;fp=secondarystructurecommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=4e7bdea09cac0d1bd86d780eb92e499bbe9bfc69;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
deleted file mode 100644
index 4e7bdea..0000000
--- a/secondarystructurecommand.h
+++ /dev/null
@@ -1,64 +0,0 @@
-#ifndef SECONDARYSTRUCTURECHECKERCOMMAND_H
-#define SECONDARYSTRUCTURECHECKERCOMMAND_H
-
-/*
- *  secondarystructurecommand.h
- *  Mothur
- *
- *  Created by westcott on 9/18/09.
- *  Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
- 
-#include "command.hpp"
-
-/**************************************************************************************************/
-
-struct statData {
-	int pound;
-	int tilde;
-	int dash;
-	int plus;
-	int equal;
-	int loop;
-	int total;
-	statData() : pound(0), loop(0), tilde(0), dash(0), plus(0), equal(0), total(0) {};	
-};
-
-/**************************************************************************************************/
-
-
-class AlignCheckCommand : public Command {
-	
-	public:
-	
-		AlignCheckCommand(string);	
-		AlignCheckCommand();
-		~AlignCheckCommand(){}
-	
-		vector<string> setParameters();
-		string getCommandName()			{ return "align.check";				}
-		string getCommandCategory()		{ return "Sequence Processing";		}
-		string getHelpString();	
-		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, namefile;
-		bool abort;
-		int seqLength, haderror;
-		vector<string> outputNames;
-		map<string, int> nameMap;
-		
-		void readMap();
-		statData getStats(string sequence);
-};
-
-/**************************************************************************************************/
-#endif
-