chimera.slayer debugging

[mothur.git] / corraxescommand.h

diff --git a/corraxescommand.h b/corraxescommand.h
index 507399c9ca4b3b686439bf7e37e7da019244724c..5f04c6a754393bda843abdf057e0f47763fd21cf 100644 (file)
--- a/corraxescommand.h
+++ b/corraxescommand.h
@@ -11,40 +11,41 @@
  */
 
 #include "command.hpp"
-#include "sharedrabundvector.h"
 #include "sharedrabundfloatvector.h"
 #include "inputdata.h"
 
+
 class CorrAxesCommand : public Command {
 public:
        CorrAxesCommand(string);
        CorrAxesCommand();
-       ~CorrAxesCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~CorrAxesCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "corr.axes";                           }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
        
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }  
 private:
-       GlobalData* globaldata;
-       string axesfile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, method;
+
+       string axesfile, sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
        bool abort, pickedGroups;
        int numaxes;
        set<string> names;
        
        vector<string> outputNames, Groups;
-       map<string, vector<string> > outputTypes;
-       vector<SharedRAbundVector*> lookup;
        vector<SharedRAbundFloatVector*> lookupFloat;
+       vector<string> metadataLabels;
        
-       int getShared();
-       int getSharedFloat();
-       int convertToRelabund();
+       int getSharedFloat(InputData*);
+       int getMetadata();
        int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
        map<string, vector<float> > readAxes();
        int calcPearson(map<string, vector<float> >&, ofstream&);
+       int calcSpearman(map<string, vector<float> >&, ofstream&);
+       int calcKendall(map<string, vector<float> >&, ofstream&);
        
 };