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         ~MGClusterCommand();
  29         vector<string> getRequiredParameters();
  30         vector<string> getValidParameters();
  31         vector<string> getRequiredFiles();
  32         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  33         int execute();
  34         void help();
  35
  36 private:
  37         GlobalData* globaldata;
  38         ReadBlast* read;
  39         NameAssignment* nameMap;
  40         Cluster* cluster;
  41         HCluster* hcluster;
  42         ListVector* list;
  43         ListVector oldList;
  44         vector<seqDist> overlapMatrix;
  45         vector<string> outputNames;
  46         map<string, vector<string> > outputTypes;
  47
  48         string blastfile, method, namefile, overlapFile, distFile, outputDir;
  49         ofstream sabundFile, rabundFile, listFile;
  50         double cutoff;
  51         float penalty;
  52         int precision, length, precisionLength;
  53         bool abort, minWanted, hclusterWanted, merge, hard;
  54
  55         void printData(ListVector*);
  56         ListVector* mergeOPFs(map<string, int>, float);
  57         void sortHclusterFiles(string, string);
  58         vector<seqDist> getSeqs(ifstream&);
  59
  60 };
  61
  62 /**********************************************************************/
  63
  64 #endif
  65
  66
  67