added pipeline commands which involved change to command factory and command class...

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 6c1ce895ac0459b2b1e0358814bc0e30d8bfe51c..2a7908167ac1ede1d402fa26c2f9c30978b31469 100644 (file)
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -26,14 +26,19 @@ class GlobalData;
 class MatrixOutputCommand : public Command {
        
 public:
-       MatrixOutputCommand(string);    
+       MatrixOutputCommand(string);
+       MatrixOutputCommand();  
        ~MatrixOutputCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
 private:
        void printSims(ostream&);
-       void process(vector<SharedRAbundVector*>);
+       int process(vector<SharedRAbundVector*>);
        
        GlobalData* globaldata;
        ReadOTUFile* read;
@@ -42,14 +47,15 @@ private:
        InputData* input;
        ValidCalculators* validCalculator;
        vector<SharedRAbundVector*> lookup;
-       string exportFileName;
+       string exportFileName, output;
        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
+       map<string, vector<string> > outputTypes;
        
 
 };