X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=splitmatrix.h;h=7b468e998d967cde992a74b2cc0745840f60d454;hp=e38f8fc1ba7afd679a7cc308547e2e0f0c11a545;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=47faf5463d44570ad66148384763db1c8238b563

diff --git a/splitmatrix.h b/splitmatrix.h
index e38f8fc..7b468e9 100644
--- a/splitmatrix.h
+++ b/splitmatrix.h
@@ -19,7 +19,9 @@ class SplitMatrix  {
 	
 	public:
 
-		SplitMatrix(string, string, string, float, string); //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
@@ -28,12 +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;
+		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);
 };
 
 /******************************************************/