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 "globaldata.hpp"
  18 #include "cluster.hpp"
  19 #include "hcluster.h"
  20
  21 /**********************************************************************/
  22
  23 class MGClusterCommand : public Command {
  24
  25 public:
  26         MGClusterCommand(string);
  27         ~MGClusterCommand();
  28         int execute();
  29         void help();
  30
  31 private:
  32         GlobalData* globaldata;
  33         ReadBlast* read;
  34         NameAssignment* nameMap;
  35         Cluster* cluster;
  36         HCluster* hcluster;
  37         ListVector* list;
  38         ListVector oldList;
  39         vector<DistNode> overlapMatrix;
  40         DistNode next;
  41
  42
  43         string blastfile, method, namefile, overlapFile, distFile;
  44         ofstream sabundFile, rabundFile, listFile;
  45         float cutoff, penalty;
  46         int precision, length, precisionLength;
  47         bool abort, minWanted, hclusterWanted, exitedBreak, merge;
  48
  49         void printData(ListVector*);
  50         ListVector* mergeOPFs(map<string, int>, float);
  51         void sortHclusterFiles(string, string);
  52         vector<DistNode> getSeqs(ifstream&);
  53
  54 };
  55
  56 /**********************************************************************/
  57
  58 #endif
  59
  60
  61