Revert to previous commit

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
new file mode 100644 (file)
index 0000000..df0c526
--- /dev/null
+++ b/mgclustercommand.h
@@ -0,0 +1,71 @@
+#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
+
+
+