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

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
deleted file mode 100644 (file)
index 268ec31..0000000
--- a/clustercommand.h
+++ /dev/null
@@ -1,68 +0,0 @@
-#ifndef CLUSTERCOMMAND_H
-#define CLUSTERCOMMAND_H
-/*
- *  clustercommand.h
- *  Dotur
- *
- *  Created by Sarah Westcott on 1/2/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-#include "listvector.hpp"
-#include "cluster.hpp"
-#include "sparsematrix.hpp"
-
-/* The cluster() command:
-       The cluster command outputs a .list , .rabund and .sabund files.  
-       The cluster command parameter options are method, cuttoff and precision. No parameters are required.  
-       The cluster command should be in the following format: cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision).  
-       The acceptable methods are furthest, nearest and average.  If you do not provide a method the default algorythm is furthest neighbor.  
-       The cluster() command outputs three files *.list, *.rabund, and *.sabund.   */
-
-
-class ClusterCommand : public Command {
-       
-public:
-       ClusterCommand(string);
-       ClusterCommand();
-       ~ClusterCommand();
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "cluster";             }
-       string getCommandCategory()             { return "Clustering";  }
-       string getHelpString(); 
-       string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Cluster"; }
-       string getDescription()         { return "cluster your sequences into OTUs using a distance matrix"; }
-       
-       int execute(); 
-       void help() { m->mothurOut(getHelpString()); }  
-       
-private:
-       Cluster* cluster;
-       SparseMatrix* matrix;
-       ListVector* list;
-       RAbundVector* rabund;
-       RAbundVector oldRAbund;
-       ListVector oldList;
-
-       bool abort, hard, sim;
-
-       string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile;
-       double cutoff;
-       string showabund, timing;
-       int precision, length;
-       ofstream sabundFile, rabundFile, listFile;
-
-       bool print_start;
-       time_t start;
-       unsigned long loops;
-       
-       void printData(string label);
-       vector<string> outputNames;
-};
-
-#endif