X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.h;h=889586ae305ac47bdb0f2d15880507aa68655dff;hb=e98d569d630c30d1ac3608eb6337bcec4765a724;hp=9aa86d4441e5c5f1202a6d552fef31162337c00d;hpb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7;p=mothur.git

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 9aa86d4..889586a 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"
 
 /**********************************************************************/
 
@@ -24,32 +25,43 @@ 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 getOutputFileNameTag(string, string);
+	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;
 	HCluster* hcluster;
 	ListVector* list;
 	ListVector oldList;
-	vector<DistNode> overlapMatrix;
-	DistNode next;
-
+	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, exitedBreak, merge;
+	bool abort, minWanted, hclusterWanted, merge, hard;
 	
 	void printData(ListVector*);
 	ListVector* mergeOPFs(map<string, int>, float);
 	void sortHclusterFiles(string, string);
-	vector<DistNode> getSeqs(ifstream&);
+	vector<seqDist> getSeqs(ifstream&);
+    RAbundVector createRabund(ListVector, map<string, int>);
 
 };