X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitmatrix.h;h=7b468e998d967cde992a74b2cc0745840f60d454;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=95fe0dcb94939bb8968a0980a517368cb0ef8b2b;hpb=2a7d1455e8cfe4f67a7173f3a7249762c5436217;p=mothur.git

diff --git a/splitmatrix.h b/splitmatrix.h
index 95fe0dc..7b468e9 100644
--- 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);
 };
 
 /******************************************************/