X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.h;fp=mgclustercommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=df0c526f2071636e87b0c2a403d2410324a8b89d;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/mgclustercommand.h b/mgclustercommand.h
deleted file mode 100644
index df0c526..0000000
--- a/mgclustercommand.h
+++ /dev/null
@@ -1,71 +0,0 @@
-#ifndef MGCLUSTERCOMMAND_H
-#define MGCLUSTERCOMMAND_H
-
-/*
- *  mgclustercommand.h
- *  Mothur
- *
- *  Created by westcott on 12/11/09.
- *  Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "readblast.h"
-#include "sparsematrix.hpp"
-#include "nameassignment.hpp"
-#include "cluster.hpp"
-#include "hcluster.h"
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-
-/**********************************************************************/
-
-class MGClusterCommand : public Command {
-
-public:
-	MGClusterCommand(string);
-	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:
-	ReadBlast* read;
-	NameAssignment* nameMap;
-	Cluster* cluster;
-	HCluster* hcluster;
-	ListVector* list;
-	ListVector oldList;
-	vector<seqDist> overlapMatrix;
-	vector<string> outputNames;
-	
-	string blastfile, method, namefile, overlapFile, distFile, outputDir;
-	ofstream sabundFile, rabundFile, listFile;
-	double cutoff;
-	float penalty;
-	int precision, length, precisionLength;
-	bool abort, minWanted, hclusterWanted, merge, hard;
-	
-	void printData(ListVector*);
-	ListVector* mergeOPFs(map<string, int>, float);
-	void sortHclusterFiles(string, string);
-	vector<seqDist> getSeqs(ifstream&);
-
-};
-
-/**********************************************************************/
-
-#endif
-
-
-