changes while testing

[mothur.git] / splitmatrix.h

diff --git a/splitmatrix.h b/splitmatrix.h
index 5974ff1b967a5b3313bea6dcbcf967eb4b1c5023..7b468e998d967cde992a74b2cc0745840f60d454 100644 (file)
--- a/splitmatrix.h
+++ b/splitmatrix.h
@@ -19,18 +19,30 @@ class SplitMatrix  {
        
        public:
 
-               SplitMatrix(string, string, float); //column formatted distance file, namesfile, cutoff
+               SplitMatrix(string, string, string, string, float, string, bool); //column formatted distance file, namesfile, countfile, cutoff, method, large
+               SplitMatrix(string, string, string, string, float, float, string, int, bool, string); //fastafile, namefile, countfile, taxFile, taxcutoff, cutoff, method, processors, classic, 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:
-               string distFile, namefile, singleton;
-               vector< map< string, string> > dists;
-               float cutoff;
-               
                MothurOut* m;
+
+               string distFile, namefile, singleton, method, taxFile, fastafile, outputDir, countfile;
+               vector< map< string, string> > dists;
+               float cutoff, distCutoff;
+               bool large, classic;
+               int processors;
+                               
+               int splitDistance();
+               int splitClassify();
+               int splitDistanceLarge();
+               int splitDistanceRAM();
+               int splitNames(map<string, int>& groups, int, vector<string>&);
+               int splitDistanceFileByTax(map<string, int>&, int);
+               int createDistanceFilesFromTax(map<string, int>&, int);
 };
 
 /******************************************************/