otuassociationcommand.h

   1 #ifndef OTUASSOCIATIONCOMMAND_H
   2 #define OTUASSOCIATIONCOMMAND_H
   3
   4 /*
   5  *  otuassociationcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 1/19/12.
   9  *  Copyright 2012 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "sharedrabundfloatvector.h"
  16 #include "inputdata.h"
  17
  18
  19 class OTUAssociationCommand : public Command {
  20 public:
  21         OTUAssociationCommand(string);
  22         OTUAssociationCommand();
  23         ~OTUAssociationCommand(){}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "otu.association";                     }
  27         string getCommandCategory()             { return "Hypothesis Testing";          }
  28         string getOutputFileNameTag(string, string);
  29         string getHelpString();
  30         string getCitation() { return "http://www.mothur.org/wiki/Otu.association"; }
  31         string getDescription()         { return "calculate the correlation coefficient for the otus in a shared/relabund file"; }
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35 private:
  36
  37         string sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
  38         bool abort, pickedGroups, allLines;
  39     double cutoff;
  40         set<string> labels;
  41     vector<SharedRAbundFloatVector*> metadataLookup;
  42     vector< vector< double> > metadata;
  43
  44         vector<string> outputNames, Groups, metadataLabels;
  45         int processShared();
  46         int process(vector<SharedRAbundVector*>&);
  47         int processRelabund();
  48         int process(vector<SharedRAbundFloatVector*>&);
  49     int readMetadata();
  50     int getMetadata();
  51
  52 };
  53
  54
  55 #endif
  56
  57
  58