adding more error checking for list and group files. outputs missing.names or missin...

[mothur.git] / secondarystructurecommand.h

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(){};
+               int execute();
+               void help();    
+               
+       private:
+               vector<int> structMap;
+               string mapfile, fastafile;
+               bool abort;
+               int seqLength;
+               
+               void readMap();
+};
+
+/**************************************************************************************************/
+#endif
+