splitmatrix.h

   1 #ifndef SPLITMATRIX_H
   2 #define SPLITMATRIX_H
   3 /*
   4  *  splitmatrix.h
   5  *  Mothur
   6  *
   7  *  Created by westcott on 5/19/10.
   8  *  Copyright 2010 Schloss Lab. All rights reserved.
   9  *
  10  */
  11
  12
  13 #include "mothur.h"
  14 #include "mothurout.h"
  15
  16 /******************************************************/
  17
  18 class SplitMatrix  {
  19
  20         public:
  21
  22                 SplitMatrix(string, string, string, string, float, string, bool); //column formatted distance file, namesfile, countfile, cutoff, method, large
  23                 SplitMatrix(string, string, string, string, float, float, string, int, bool, string); //fastafile, namefile, countfile, taxFile, taxcutoff, cutoff, method, processors, classic, outputDir
  24
  25                 ~SplitMatrix();
  26                 int split();
  27                 vector< map<string, string> > getDistanceFiles();  //returns map of distance files -> namefile sorted by distance file size
  28                 string getSingletonNames() { return singleton; } //returns namesfile containing singletons
  29
  30         private:
  31                 MothurOut* m;
  32
  33                 string distFile, namefile, singleton, method, taxFile, fastafile, outputDir, countfile;
  34                 vector< map< string, string> > dists;
  35                 float cutoff, distCutoff;
  36                 bool large, classic;
  37                 int processors;
  38
  39                 int splitDistance();
  40                 int splitClassify();
  41                 int splitDistanceLarge();
  42                 int splitDistanceRAM();
  43                 int splitNames(map<string, int>& groups, int, vector<string>&);
  44                 int splitDistanceFileByTax(map<string, int>&, int);
  45                 int createDistanceFilesFromTax(map<string, int>&, int);
  46 };
  47
  48 /******************************************************/
  49
  50 #endif
  51