X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.h;h=df0c526f2071636e87b0c2a403d2410324a8b89d;hb=94d43af803e4be78b2ba8049669504e854ad13be;hp=2ac80c91dd65fa7cf56f71331e4c4486c68c8b87;hpb=b5a791c81d432082bf38755a08b33863f255341d;p=mothur.git

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 2ac80c9..df0c526 100644
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -14,9 +14,10 @@
 #include "readblast.h"
 #include "sparsematrix.hpp"
 #include "nameassignment.hpp"
-#include "globaldata.hpp"
 #include "cluster.hpp"
 #include "hcluster.h"
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
 
 /**********************************************************************/
 
@@ -24,12 +25,21 @@ class MGClusterCommand : public Command {
 
 public:
 	MGClusterCommand(string);
-	~MGClusterCommand();
-	int execute();
-	void help();
+	MGClusterCommand();
+	~MGClusterCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "mgcluster";	}
+	string getCommandCategory()		{ return "Clustering";	}
+	string getHelpString();	
+	string getCitation() { return "Schloss PD, Handelsman J (2008). A statistical toolbox for metagenomics. BMC Bioinformatics 9: 34. \nhttp://www.mothur.org/wiki/Mgcluster"; }
+	string getDescription()		{ return "cluster your sequences into OTUs using a blast file"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
 	ReadBlast* read;
 	NameAssignment* nameMap;
 	Cluster* cluster;
@@ -37,12 +47,14 @@ private:
 	ListVector* list;
 	ListVector oldList;
 	vector<seqDist> overlapMatrix;
+	vector<string> outputNames;
 	
-	string blastfile, method, namefile, overlapFile, distFile;
+	string blastfile, method, namefile, overlapFile, distFile, outputDir;
 	ofstream sabundFile, rabundFile, listFile;
-	float cutoff, penalty;
+	double cutoff;
+	float penalty;
 	int precision, length, precisionLength;
-	bool abort, minWanted, hclusterWanted, merge;
+	bool abort, minWanted, hclusterWanted, merge, hard;
 	
 	void printData(ListVector*);
 	ListVector* mergeOPFs(map<string, int>, float);