1 #ifndef METASTATSCOMMAND_H 2 #define METASTATSCOMMAND_H 3 4 /* 5 * metastatscommand.h 6 * Mothur 7 * 8 * Created by westcott on 9/16/10. 9 * Copyright 2010 Schloss Lab. All rights reserved. 10 * 11 */ 12 13 #include "command.hpp" 14 #include "inputdata.h" 15 #include "sharedrabundvectors.hpp" 16 #include "sharedclrvectors.hpp" 17 #include "mothurmetastats.h" 18 #include "designmap.h" 19 20 21 /**************************************************************************************************/ 22 23 class MetaStatsCommand : public Command { 24 25 public: 26 MetaStatsCommand(string); ~MetaStatsCommand()27 ~MetaStatsCommand() {} 28 29 vector<string> setParameters(); getCommandName()30 string getCommandName() { return "metastats"; } getCommandCategory()31 string getCommandCategory() { return "OTU-Based Approaches"; } 32 33 string getHelpString(); 34 string getOutputPattern(string); getCitation()35 string getCitation() { return "White JR, Nagarajan N, Pop M (2009). Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352. \nhttp://www.mothur.org/wiki/Metastats"; } getDescription()36 string getDescription() { return "detects differentially abundant features in clinical metagenomic samples"; } 37 38 int execute(); help()39 void help() { m->mothurOut(getHelpString()); } 40 41 private: 42 43 bool abort, allLines, pickedGroups; 44 set<string> labels; //holds labels to be used 45 string groups, label, inputDir, designfile, sets, sharedfile, clrfile, inputfile, format; 46 vector<string> Groups, outputNames, Sets; 47 vector< vector<string> > namesOfGroupCombos; 48 int iters, processors; 49 float threshold; 50 51 int process(SharedRAbundVectors*&, DesignMap*&); 52 int process(SharedCLRVectors*&, DesignMap*&); 53 }; 54 55 /**************************************************************************************************/ 56 57 #endif 58 59