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
  36         int execute();
  37         void help() { m->mothurOut(getHelpString()); }
  38
  39
  40 private:
  41         ReadBlast* read;
  42         NameAssignment* nameMap;
  43         Cluster* cluster;
  44         HCluster* hcluster;
  45         ListVector* list;
  46         ListVector oldList;
  47         vector<seqDist> overlapMatrix;
  48         vector<string> outputNames;
  49
  50         string blastfile, method, namefile, overlapFile, distFile, outputDir;
  51         ofstream sabundFile, rabundFile, listFile;
  52         double cutoff;
  53         float penalty;
  54         int precision, length, precisionLength;
  55         bool abort, minWanted, hclusterWanted, merge, hard;
  56
  57         void printData(ListVector*);
  58         ListVector* mergeOPFs(map<string, int>, float);
  59         void sortHclusterFiles(string, string);
  60         vector<seqDist> getSeqs(ifstream&);
  61
  62 };
  63
  64 /**********************************************************************/
  65
  66 #endif
  67
  68
  69