added Jensen-Shannon calc. working on get.communitytype command. fixed bug in get...

[mothur.git] / summarysharedcommand.h

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index f486d520216bd8ec4858d50cd7f2d92b7fd23537..1b3f16469bfc64345631f489e4c6651895041de0 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -56,6 +56,7 @@
 #include "memchord.h"
 #include "memeuclidean.h"
 #include "mempearson.h"
+#include "sharedjsd.h"
 
 class SummarySharedCommand : public Command {
 
@@ -112,6 +113,7 @@ 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) {
@@ -121,6 +123,7 @@ struct summarySharedData {
                end = en;
         Estimators = est;
         thisLookup = lu;
+        count=0;
        }
 };
 /**************************************************************************************************/
@@ -214,6 +217,8 @@ 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());
                 }
             }
         }
@@ -225,7 +230,7 @@ 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';