-#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
-