working on citations

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 02e8fe6b4cb75351fadfc5a503b78ed6bd589a7d..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;
-       vector<string>  Estimators, Groups; //holds estimators to be used
-       
-
+       string outputFile, calc, groups, label, outputDir;
+       vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
 };