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
  20
  21 class ClusterSplitCommand : public Command {
  22
  23 public:
  24         ClusterSplitCommand(string);
  25         ClusterSplitCommand();
  26         ~ClusterSplitCommand() {}
  27
  28         vector<string> setParameters();
  29         string getCommandName()                 { return "cluster.split";               }
  30         string getCommandCategory()             { return "Clustering";                  }
  31         string getHelpString();
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37         vector<int> processIDS;   //processid
  38         vector<string> outputNames;
  39
  40         string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
  41         double cutoff, splitcutoff;
  42         int precision, length, processors, taxLevelCutoff;
  43         bool print_start, abort, hard, large;
  44         time_t start;
  45         ofstream outList, outRabund, outSabund;
  46
  47         void printData(ListVector*);
  48         int createProcesses(vector < vector < map<string, string> > >);
  49         vector<string> cluster(vector< map<string, string> >, set<string>&);
  50         int mergeLists(vector<string>, map<float, int>, ListVector*);
  51         map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
  52         int createMergedDistanceFile(vector< map<string, string> >);
  53 };
  54
  55 #endif
  56