X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.h;h=7a2a1909368fc9c71edbcbc90add7d3a966ac95d;hb=a65438a717aba8cad1ff86c53279b191710b8810;hp=7c6a4b2965783a8145d311cfae05a150d82c2ce7;hpb=f687723a8357916e86a05116978e6869b039ce36;p=mothur.git

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 7c6a4b2..7a2a190 100644
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -56,6 +56,8 @@
 #include "memchord.h"
 #include "memeuclidean.h"
 #include "mempearson.h"
+#include "sharedjsd.h"
+#include "sharedrjsd.h"
 
 class SummarySharedCommand : public Command {
 
@@ -67,8 +69,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "summary.shared";			}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
 	string getDescription()		{ return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
 
@@ -111,6 +114,7 @@ struct summarySharedData {
 	unsigned long long end;
 	MothurOut* m;
 	string sumFile;
+    int count;
 	
 	summarySharedData(){}
 	summarySharedData(string sf, MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
@@ -120,6 +124,7 @@ struct summarySharedData {
 		end = en;
         Estimators = est;
         thisLookup = lu;
+        count=0;
 	}
 };
 /**************************************************************************************************/
@@ -213,6 +218,10 @@ static DWORD WINAPI MySummarySharedThreadFunction(LPVOID lpParam){
                     sumCalculators.push_back(new MemEuclidean());
                 }else if (pDataArray->Estimators[i] == "mempearson") { 
                     sumCalculators.push_back(new MemPearson());
+                }else if (pDataArray->Estimators[i] == "jsd") {
+                    sumCalculators.push_back(new JSD());
+                }else if (pDataArray->Estimators[i] == "rjsd") {
+                    sumCalculators.push_back(new RJSD());
                 }
             }
         }
@@ -224,7 +233,7 @@ static DWORD WINAPI MySummarySharedThreadFunction(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++) {
 				
 				outputFileHandle << pDataArray->thisLookup[0]->getLabel() << '\t';