X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=splitmatrix.h;h=7b468e998d967cde992a74b2cc0745840f60d454;hp=5974ff1b967a5b3313bea6dcbcf967eb4b1c5023;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=725a3d4ff2442c79bfde0a75ed3e0904edcf03b7

diff --git a/splitmatrix.h b/splitmatrix.h
index 5974ff1..7b468e9 100644
--- 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);
 };
 
 /******************************************************/