X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=matrixoutputcommand.h;h=90f120602e70dc04600b3048bab41bde21b21edc;hp=ff05ef70a30736f661379608ecd291e388cf9301;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index ff05ef7..90f1206 100644
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -73,8 +73,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "dist.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
 	string getDescription()		{ return "generate a distance matrix that describes the dissimilarity among multiple groups"; }
 
@@ -120,6 +121,7 @@ struct distSharedData {
 	unsigned long long start;
 	unsigned long long end;
 	MothurOut* m;
+    int count;
 	
 	distSharedData(){}
 	distSharedData(MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
@@ -128,6 +130,7 @@ struct distSharedData {
 		end = en;
         Estimators = est;
         thisLookup = lu;
+        count = 0;
 	}
 };
 /**************************************************************************************************/
@@ -229,7 +232,7 @@ static DWORD WINAPI MyDistSharedThreadFunction(LPVOID lpParam){
         		
 		vector<SharedRAbundVector*> subset;
 		for (int k = pDataArray->start; k < pDataArray->end; k++) { // pass cdd each set of groups to compare
-			
+			pDataArray->count++;
 			for (int l = 0; l < k; l++) {
 				
 				if (k != l) { //we dont need to similiarity of a groups to itself