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         ~ClusterSplitCommand();
  28         vector<string> getRequiredParameters();
  29         vector<string> getValidParameters();
  30         vector<string> getRequiredFiles();
  31         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  32         int execute();
  33         void help();
  34
  35 private:
  36         GlobalData* globaldata;
  37         vector<int> processIDS;   //processid
  38         vector<string> outputNames;
  39         map<string, vector<string> > outputTypes;
  40
  41         string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
  42         double cutoff, splitcutoff;
  43         int precision, length, processors, taxLevelCutoff;
  44         bool print_start, abort, hard, large;
  45         time_t start;
  46         ofstream outList, outRabund, outSabund;
  47
  48         void printData(ListVector*);
  49         int createProcesses(vector < vector < map<string, string> > >);
  50         vector<string> cluster(vector< map<string, string> >, set<string>&);
  51         int mergeLists(vector<string>, map<float, int>, ListVector*);
  52         map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
  53 };
  54
  55 #endif
  56