modified chop.seqs

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 02e8fe6b4cb75351fadfc5a503b78ed6bd589a7d..537f7916299d36c7f628a9e7e6974821746f3b12 100644 (file)
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -33,7 +33,7 @@ public:
        
 private:
        void printSims(ostream&);
-       void process(vector<SharedRAbundVector*>);
+       int process(vector<SharedRAbundVector*>);
        
        GlobalData* globaldata;
        ReadOTUFile* read;
@@ -42,14 +42,14 @@ 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;
-       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
        
 
 };