1 #ifndef SECONDARYSTRUCTURECHECKERCOMMAND_H
2 #define SECONDARYSTRUCTURECHECKERCOMMAND_H
5 * secondarystructurecommand.h
8 * Created by westcott on 9/18/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
13 #include "command.hpp"
15 /**************************************************************************************************/
25 statData() : pound(0), loop(0), tilde(0), dash(0), plus(0), equal(0), total(0) {};
28 /**************************************************************************************************/
31 class AlignCheckCommand : public Command {
35 AlignCheckCommand(string);
37 ~AlignCheckCommand(){}
39 vector<string> setParameters();
40 string getCommandName() { return "align.check"; }
41 string getCommandCategory() { return "Sequence Processing"; }
42 string getHelpString();
43 string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
44 string getDescription() { return "calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment"; }
48 void help() { m->mothurOut(getHelpString()); }
51 vector<int> structMap;
52 string mapfile, fastafile, outputDir, namefile;
54 int seqLength, haderror;
55 vector<string> outputNames;
56 map<string, int> nameMap;
59 statData getStats(string sequence);
62 /**************************************************************************************************/