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[mothur.git] / splitmatrix.h

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+#ifndef SPLITMATRIX_H
+#define SPLITMATRIX_H
+/*
+ *  splitmatrix.h
+ *  Mothur
+ *
+ *  Created by westcott on 5/19/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "mothur.h"
+#include "mothurout.h"
+
+/******************************************************/
+
+class SplitMatrix  {
+       
+       public:
+
+               SplitMatrix(string, string, string, float, string, bool); //column formatted distance file, namesfile, cutoff, method, large
+               SplitMatrix(string, string, string, float, float, string, int, string); //fastafile, namefile, taxFile, taxcutoff, cutoff, method, processors, outputDir
+               
+               ~SplitMatrix();
+               int split();
+               vector< map<string, string> > getDistanceFiles();  //returns map of distance files -> namefile sorted by distance file size
+               string getSingletonNames() { return singleton; } //returns namesfile containing singletons
+       
+       private:
+               MothurOut* m;
+
+               string distFile, namefile, singleton, method, taxFile, fastafile, outputDir;
+               vector< map< string, string> > dists;
+               float cutoff, distCutoff;
+               bool large;
+               int processors;
+                               
+               int splitDistance();
+               int splitClassify();
+               int splitDistanceLarge();
+               int splitDistanceRAM();
+               int splitNames(vector<set<string> >& groups);
+               int splitDistanceFileByTax(map<string, int>&, int);
+               int createDistanceFilesFromTax(map<string, int>&, int);
+};
+
+/******************************************************/
+
+#endif
+