X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.h;h=8a04c96a32ed6fa769a4e14474dfb624451751d1;hb=0bd3a2d33b478f0b09fd6b8ce562e9ab41227535;hp=dc77bdf067ff194dce8bd2e5fcb8f078a9450dcc;hpb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;p=mothur.git

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index dc77bdf..8a04c96 100644
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -73,7 +73,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "dist.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	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 +90,7 @@ private:
 	};
 	vector<linePair> lines;
 	
-	void printSims(ostream&, vector< vector<float> >&);
+	void printSims(ostream&, vector< vector<double> >&);
 	int process(vector<SharedRAbundVector*>);
 	
 	vector<Calculator*> matrixCalculators;
@@ -96,12 +98,12 @@ 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;
+	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> >&);