X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.h;h=ff05ef70a30736f661379608ecd291e388cf9301;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=f915dfcda8d7ab88040fcb1e8e2f4bbabf833590;hpb=53171f07cc0c0e560e2b4ba2946f690d59fc2dc4;p=mothur.git

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index f915dfc..ff05ef7 100644
--- 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"; }
@@ -88,7 +89,7 @@ private:
 	};
 	vector<linePair> lines;
 	
-	void printSims(ostream&, vector< vector<float> >&);
+	void printSims(ostream&, vector< vector<double> >&);
 	int process(vector<SharedRAbundVector*>);
 	
 	vector<Calculator*> matrixCalculators;
@@ -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> >&);