X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=splitmatrix.h;h=7b468e998d967cde992a74b2cc0745840f60d454;hp=acaa8c5b711a220e76e48be2fc983122514d6b32;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=814675616c10a40911886afb9dfe216f0245e3a2

diff --git a/splitmatrix.h b/splitmatrix.h
index acaa8c5..7b468e9 100644
--- a/splitmatrix.h
+++ b/splitmatrix.h
@@ -19,8 +19,8 @@ class SplitMatrix  {
 	
 	public:
 
-		SplitMatrix(string, string, string, float, string, bool); //column formatted distance file, namesfile, cutoff, method, large
-		SplitMatrix(string, string, string, float, string, int, string); //fastafile, namefile, taxFile, cutoff, method, processors, outputDir
+		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();
@@ -30,17 +30,17 @@ class SplitMatrix  {
 	private:
 		MothurOut* m;
 
-		string distFile, namefile, singleton, method, taxFile, fastafile, outputDir;
+		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);
 };