X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mgclustercommand.h;h=3865bb20811a0ac29e29e0fec02392268ea0a657;hp=9aa86d4441e5c5f1202a6d552fef31162337c00d;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 9aa86d4..3865bb2 100644
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -12,11 +12,12 @@
 
 #include "command.hpp"
 #include "readblast.h"
-#include "sparsematrix.hpp"
 #include "nameassignment.hpp"
-#include "globaldata.hpp"
 #include "cluster.hpp"
 #include "hcluster.h"
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "counttable.h"
 
 /**********************************************************************/
 
@@ -24,32 +25,46 @@ 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 getOutputPattern(string);	
+	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;
+    CountTable* ct;
 	ListVector oldList;
-	vector<DistNode> overlapMatrix;
-	DistNode next;
-
+    RAbundVector rav;
+	vector<seqDist> overlapMatrix;
+	vector<string> outputNames;
 	
-	string blastfile, method, namefile, overlapFile, distFile;
+	string blastfile, method, namefile, countfile, overlapFile, distFile, outputDir;
 	ofstream sabundFile, rabundFile, listFile;
-	float cutoff, penalty;
+	double cutoff;
+	float penalty, adjust;
 	int precision, length, precisionLength;
-	bool abort, minWanted, hclusterWanted, exitedBreak, merge;
+	bool abort, minWanted, hclusterWanted, merge, hard, cutoffSet;
 	
 	void printData(ListVector*);
 	ListVector* mergeOPFs(map<string, int>, float);
 	void sortHclusterFiles(string, string);
-	vector<DistNode> getSeqs(ifstream&);
+	vector<seqDist> getSeqs(ifstream&);
+    void createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 
 };