X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.h;h=ae38b46c5c1d60a1c6c97b5a618f1eca8d59a417;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=40706b96581ba3d72f76b5efc8783788f7d60102;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 40706b9..ae38b46 100644
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -32,27 +32,38 @@ public:
 	string getCommandName()			{ return "dist.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
 	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"; }
+
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	void printSims(ostream&);
+	struct linePair {
+		int start;
+		int end;
+	};
+	vector<linePair> lines;
+	
+	void printSims(ostream&, vector< vector<float> >&);
 	int process(vector<SharedRAbundVector*>);
 	
 	vector<Calculator*> matrixCalculators;
-	vector< vector<float> > simMatrix;
+	//vector< vector<float> > simMatrix;
 	InputData* input;
-	ValidCalculators* validCalculator;
 	vector<SharedRAbundVector*> lookup;
 	string exportFileName, output, sharedfile;
-	int numGroups;
+	int numGroups, processors;
 	ofstream out;
 
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used
 	string outputFile, calc, groups, label, outputDir;
 	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> >&);
+
 };