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
  29         string getHelpString();
  30     string getOutputPattern(string);
  31         string getCitation() { return "http://www.mothur.org/wiki/Otu.association"; }
  32         string getDescription()         { return "calculate the correlation coefficient for the otus in a shared/relabund file"; }
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36 private:
  37
  38         string sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
  39         bool abort, pickedGroups, allLines;
  40     double cutoff;
  41         set<string> labels;
  42     vector<SharedRAbundFloatVector*> metadataLookup;
  43     vector< vector< double> > metadata;
  44
  45         vector<string> outputNames, Groups, metadataLabels;
  46         int processShared();
  47         int process(vector<SharedRAbundVector*>&);
  48         int processRelabund();
  49         int process(vector<SharedRAbundFloatVector*>&);
  50     int readMetadata();
  51     int getMetadata();
  52
  53 };
  54
  55
  56 #endif
  57
  58
  59