Merge remote-tracking branch 'origin/master'

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 8af539ba01ae59ed07027d63f2bd9d1859b4c217..ff05ef70a30736f661379608ecd291e388cf9301 100644 (file)
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -73,6 +73,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "dist.shared";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
        string getDescription()         { return "generate a distance matrix that describes the dissimilarity among multiple groups"; }
@@ -101,7 +102,7 @@ private:
 
        bool abort, allLines, subsample;
        set<string> labels; //holds labels to be used
-       string outputFile, calc, groups, label, outputDir;
+       string outputFile, calc, groups, label, outputDir, mode;
        vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
        int process(vector<SharedRAbundVector*>, string, string);
        int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);