X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;fp=secondarystructurecommand.h;h=d94cc95582f8d1482233a3cac0aee4b418dcc925;hb=462fca6d24fd15ca035358ff70bcfae52c3281c3;hp=0000000000000000000000000000000000000000;hpb=98ea55ba2d46a429f031086b4b3272780d0ec894;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
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+#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(){};
+		int execute();
+		void help();	
+		
+	private:
+		vector<int> structMap;
+		string mapfile, fastafile;
+		bool abort;
+		int seqLength;
+		
+		void readMap();
+};
+
+/**************************************************************************************************/
+#endif
+