moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
deleted file mode 100644 (file)
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
-
-
-