working on citations

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 2a7908167ac1ede1d402fa26c2f9c30978b31469..2c403aa1570895546ea1cbeb8e6c2e46d406c7e3 100644 (file)
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -12,7 +12,6 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
 // aka. dist.shared()
@@ -21,7 +20,6 @@
        The user can select the labels they wish to use as well as the groups they would like included.
        They can also use as many or as few calculators as they wish. */
        
-class GlobalData;
 
 class MatrixOutputCommand : public Command {
        
@@ -29,25 +27,25 @@ public:
        MatrixOutputCommand(string);
        MatrixOutputCommand();  
        ~MatrixOutputCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "dist.shared";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        void printSims(ostream&);
        int process(vector<SharedRAbundVector*>);
        
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        vector<Calculator*> matrixCalculators;
        vector< vector<float> > simMatrix;
        InputData* input;
-       ValidCalculators* validCalculator;
        vector<SharedRAbundVector*> lookup;
-       string exportFileName, output;
+       string exportFileName, output, sharedfile;
        int numGroups;
        ofstream out;
 
@@ -55,9 +53,6 @@ private:
        set<string> labels; //holds labels to be used
        string outputFile, calc, groups, label, outputDir;
        vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
-       map<string, vector<string> > outputTypes;
-       
-
 };