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[mothur.git] / secondarystructurecommand.h

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();
+               ~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
+