clustersplitcommand.h

   1 #ifndef CLUSTERSPLITCOMMAND_H
   2 #define CLUSTERSPLITCOMMAND_H
   3
   4 /*
   5  *  clustersplitcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 5/19/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "rabundvector.hpp"
  15 #include "sabundvector.hpp"
  16 #include "listvector.hpp"
  17 #include "cluster.hpp"
  18 #include "sparsematrix.hpp"
  19 #include "globaldata.hpp"
  20
  21
  22 class ClusterSplitCommand : public Command {
  23
  24 public:
  25         ClusterSplitCommand(string);
  26         ~ClusterSplitCommand();
  27         int execute();
  28         void help();
  29
  30 private:
  31         GlobalData* globaldata;
  32         vector<int> processIDS;   //processid
  33         vector<string> outputNames;
  34
  35         string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile;
  36         double cutoff, splitcutoff;
  37         int precision, length, processors, taxLevelCutoff;
  38         bool print_start, abort, hard, large;
  39         time_t start;
  40         ofstream outList, outRabund, outSabund;
  41
  42         void printData(ListVector*);
  43         int createProcesses(vector < vector < map<string, string> > >);
  44         vector<string> cluster(vector< map<string, string> >, set<string>&);
  45         int mergeLists(vector<string>, map<float, int>, ListVector*);
  46         map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
  47 };
  48
  49 #endif
  50