X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;fp=secondarystructurecommand.h;h=4e7bdea09cac0d1bd86d780eb92e499bbe9bfc69;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
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+++ 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();
+		~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
+