5 // Created by SarahsWork on 5/14/13.
6 // Copyright (c) 2013 Schloss Lab. All rights reserved.
9 #ifndef Mothur_makelookupcommand_h
10 #define Mothur_makelookupcommand_h
12 #include "command.hpp"
13 #include "sequence.hpp"
15 /**************************************************************************************************/
17 class MakeLookupCommand : public Command {
19 MakeLookupCommand(string);
21 ~MakeLookupCommand(){}
23 vector<string> setParameters();
24 string getCommandName() { return "make.lookup"; }
25 string getCommandCategory() { return "Sequence Processing"; }
27 string getOutputPattern(string);
28 string getHelpString();
29 string getCitation() { return "http://www.mothur.org/wiki/Make.lookup"; }
30 string getDescription() { return "create custom lookup files for use with shhh.flows"; }
33 void help() { m->mothurOut(getHelpString()); }
37 string outputDir, flowFileName, errorFileName, flowOrder, refFastaFileName, barcodeSequence, keySequence;
38 vector<string> outputNames;
41 vector<double> convertSeqToFlow(string sequence, string order);
42 int alignFlowGrams(vector<double>& flowgram, vector<double>& refFlow, double gapOpening, vector<vector<double> > penaltyMatrix, string flowOrder);
43 int regress(vector<double>& data, int N);
46 /**************************************************************************************************/