X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.h;h=a19ffc813945e7d8b9ead51a716149881091ad2f;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=8a04c96a32ed6fa769a4e14474dfb624451751d1;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;p=mothur.git

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 8a04c96..a19ffc8 100644
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -54,6 +54,8 @@
 #include "memchord.h"
 #include "memeuclidean.h"
 #include "mempearson.h"
+#include "sharedjsd.h"
+#include "sharedrjsd.h"
 
 
 // aka. dist.shared()
@@ -121,6 +123,7 @@ 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) {
@@ -129,6 +132,7 @@ struct distSharedData {
 		end = en;
         Estimators = est;
         thisLookup = lu;
+        count = 0;
 	}
 };
 /**************************************************************************************************/
@@ -222,7 +226,12 @@ static DWORD WINAPI MyDistSharedThreadFunction(LPVOID lpParam){
                     matrixCalculators.push_back(new MemEuclidean());
                 }else if (pDataArray->Estimators[i] == "mempearson") { 
                     matrixCalculators.push_back(new MemPearson());
+                }else if (pDataArray->Estimators[i] == "jsd") {
+                    matrixCalculators.push_back(new JSD());
+                }else if (pDataArray->Estimators[i] == "rjsd") {
+                    matrixCalculators.push_back(new RJSD());
                 }
+
             }
         }
         
@@ -230,7 +239,7 @@ 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