changes while testing

[mothur.git] / splitmatrix.h

diff --git a/splitmatrix.h b/splitmatrix.h
index 95fe0dcb94939bb8968a0980a517368cb0ef8b2b..7b468e998d967cde992a74b2cc0745840f60d454 100644 (file)
--- a/splitmatrix.h
+++ b/splitmatrix.h
@@ -19,7 +19,9 @@ class SplitMatrix  {
        
        public:
 
-               SplitMatrix(string, string, string, float, string, bool); //column formatted distance file, namesfile, cutoff, method
+               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
@@ -28,16 +30,19 @@ class SplitMatrix  {
        private:
                MothurOut* m;
 
-               string distFile, namefile, singleton, method, taxFile;
+               string distFile, namefile, singleton, method, taxFile, fastafile, outputDir, countfile;
                vector< map< string, string> > dists;
-               float cutoff;
-               bool large;
+               float cutoff, distCutoff;
+               bool large, classic;
+               int processors;
                                
                int splitDistance();
                int splitClassify();
                int splitDistanceLarge();
                int splitDistanceRAM();
-               int splitNames(vector<set<string> >& groups);
+               int splitNames(map<string, int>& groups, int, vector<string>&);
+               int splitDistanceFileByTax(map<string, int>&, int);
+               int createDistanceFilesFromTax(map<string, int>&, int);
 };
 
 /******************************************************/