added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index dc77bdf067ff194dce8bd2e5fcb8f078a9450dcc..8af539ba01ae59ed07027d63f2bd9d1859b4c217 100644 (file)
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -88,7 +88,7 @@ private:
        };
        vector<linePair> lines;
        
-       void printSims(ostream&, vector< vector<float> >&);
+       void printSims(ostream&, vector< vector<double> >&);
        int process(vector<SharedRAbundVector*>);
        
        vector<Calculator*> matrixCalculators;
@@ -96,10 +96,10 @@ private:
        InputData* input;
        vector<SharedRAbundVector*> lookup;
        string exportFileName, output, sharedfile;
-       int numGroups, processors;
+       int numGroups, processors, iters, subsampleSize;
        ofstream out;
 
-       bool abort, allLines;
+       bool abort, allLines, subsample;
        set<string> labels; //holds labels to be used
        string outputFile, calc, groups, label, outputDir;
        vector<string>  Estimators, Groups, outputNames; //holds estimators to be used