X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mgclustercommand.h;h=008bd222a0a91869e14895738ea852b383c0395f;hp=4ef0bd90de3de904e51556e87e31163f4d08d0c7;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=47faf5463d44570ad66148384763db1c8238b563

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 4ef0bd9..008bd22 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"
 
 /**********************************************************************/
 
@@ -24,21 +25,35 @@ 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;
+    RAbundVector rav;
 	vector<seqDist> overlapMatrix;
+	vector<string> outputNames;
 	
-	string blastfile, method, namefile, overlapFile, distFile, outputDir;
+	string blastfile, method, namefile, countfile, overlapFile, distFile, outputDir;
 	ofstream sabundFile, rabundFile, listFile;
 	double cutoff;
 	float penalty;
@@ -49,6 +64,7 @@ private:
 	ListVector* mergeOPFs(map<string, int>, float);
 	void sortHclusterFiles(string, string);
 	vector<seqDist> getSeqs(ifstream&);
+    void createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 
 };