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(){}
38 vector<string> getRequiredParameters();
39 vector<string> getValidParameters();
40 vector<string> getRequiredFiles();
41 map<string, vector<string> > getOutputFiles() { return outputTypes; }
46 vector<int> structMap;
47 string mapfile, fastafile, outputDir;
49 int seqLength, haderror;
50 vector<string> outputNames;
51 map<string, vector<string> > outputTypes;
54 statData getStats(string sequence);
57 /**************************************************************************************************/