working on citations

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 6c1ce895ac0459b2b1e0358814bc0e30d8bfe51c..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()
@@ -21,37 +20,39 @@
        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 {
        
 public:
-       MatrixOutputCommand(string);    
+       MatrixOutputCommand(string);
+       MatrixOutputCommand();  
        ~MatrixOutputCommand();
-       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&);
-       void process(vector<SharedRAbundVector*>);
+       int process(vector<SharedRAbundVector*>);
        
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        vector<Calculator*> matrixCalculators;
        vector< vector<float> > simMatrix;
        InputData* input;
-       ValidCalculators* validCalculator;
        vector<SharedRAbundVector*> lookup;
-       string exportFileName;
+       string exportFileName, output, sharedfile;
        int numGroups;
        ofstream out;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used
        string outputFile, calc, groups, label, outputDir;
-       vector<string>  Estimators, Groups; //holds estimators to be used
-       
-
+       vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
 };