mgclustercommand.h

   1 #ifndef MGCLUSTERCOMMAND_H
   2 #define MGCLUSTERCOMMAND_H
   3
   4 /*
   5  *  mgclustercommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 12/11/09.
   9  *  Copyright 2009 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "readblast.h"
  15 #include "sparsematrix.hpp"
  16 #include "nameassignment.hpp"
  17 #include "cluster.hpp"
  18 #include "hcluster.h"
  19 #include "rabundvector.hpp"
  20 #include "sabundvector.hpp"
  21
  22 /**********************************************************************/
  23
  24 class MGClusterCommand : public Command {
  25
  26 public:
  27         MGClusterCommand(string);
  28         MGClusterCommand();
  29         ~MGClusterCommand(){}
  30
  31         vector<string> setParameters();
  32         string getCommandName()                 { return "mgcluster";   }
  33         string getCommandCategory()             { return "Clustering";  }
  34         string getHelpString();
  35         string getCitation() { return "http://www.mothur.org/wiki/Mgcluster"; }
  36
  37         int execute();
  38         void help() { m->mothurOut(getHelpString()); }
  39
  40
  41 private:
  42         ReadBlast* read;
  43         NameAssignment* nameMap;
  44         Cluster* cluster;
  45         HCluster* hcluster;
  46         ListVector* list;
  47         ListVector oldList;
  48         vector<seqDist> overlapMatrix;
  49         vector<string> outputNames;
  50
  51         string blastfile, method, namefile, overlapFile, distFile, outputDir;
  52         ofstream sabundFile, rabundFile, listFile;
  53         double cutoff;
  54         float penalty;
  55         int precision, length, precisionLength;
  56         bool abort, minWanted, hclusterWanted, merge, hard;
  57
  58         void printData(ListVector*);
  59         ListVector* mergeOPFs(map<string, int>, float);
  60         void sortHclusterFiles(string, string);
  61         vector<seqDist> getSeqs(ifstream&);
  62
  63 };
  64
  65 /**********************************************************************/
  66
  67 #endif
  68
  69
  70