1 #ifndef SUMMARYQUALCOMMAND_H 2 #define SUMMARYQUALCOMMAND_H 3 4 /* 5 * summaryqualcommand.h 6 * Mothur 7 * 8 * Created by westcott on 11/28/11. 9 * Copyright 2011 Schloss Lab. All rights reserved. 10 * 11 */ 12 13 14 #include "command.hpp" 15 #include "qualityscores.h" 16 17 /**************************************************************************************************/ 18 19 class SummaryQualCommand : public Command { 20 public: 21 SummaryQualCommand(string); 22 ~SummaryQualCommand()23 ~SummaryQualCommand(){} 24 25 vector<string> setParameters(); getCommandName()26 string getCommandName() { return "summary.qual"; } getCommandCategory()27 string getCommandCategory() { return "Sequence Processing"; } 28 29 string getHelpString(); 30 string getOutputPattern(string); getCitation()31 string getCitation() { return "http://www.mothur.org/wiki/Summary.qual"; } getDescription()32 string getDescription() { return "summarize the quality of a set of sequences"; } 33 34 int execute(); help()35 void help() { m->mothurOut(getHelpString()); } 36 37 private: 38 bool abort, hasNameMap; 39 string qualfile, namefile, countfile; 40 vector<string> outputNames; 41 map<string, int> nameMap; 42 int processors; 43 44 long long createProcessesCreateSummary(vector<int>&, vector<int>&, vector< vector<int> >&, string); 45 int printQual(string, vector<int>&, vector<int>&, vector< vector<int> >&); 46 }; 47 /**************************************************************************************************/ 48 49 #endif 50 51