X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=1df79888eb8bdacb442b9dc2c89c51a7d4fa75ff;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=a4a1bc3defc98beb608b38645471e46541a0b10f;hpb=f55cf350ca6643f8eb070d8336e1957699a3f109;p=mothur.git

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index a4a1bc3..1df7988 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -237,6 +237,7 @@ int UnifracWeightedCommand::execute() {
         T = reader->getTrees();
         tmap = T[0]->getTreeMap();
         map<string, string> nameMap = reader->getNames();
+        map<string, string> unique2Dup = reader->getNameMap();
         delete reader;
     
         if (m->control_pressed) {  delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } return 0; }
@@ -336,11 +337,15 @@ int UnifracWeightedCommand::execute() {
                 
                 //copy to preserve old one - would do this in subsample but memory cleanup becomes messy.
                 TreeMap* newTmap = new TreeMap();
-                newTmap->getCopy(*tmap);
+                //newTmap->getCopy(*tmap);
                 
+                //SubSample sample;
+               //Tree* subSampleTree = sample.getSample(T[i], newTmap, nameMap, subsampleSize);
+                
+                //uses method of setting groups to doNotIncludeMe
                 SubSample sample;
-                Tree* subSampleTree = sample.getSample(T[i], newTmap, nameMap, subsampleSize);
-                   
+                Tree* subSampleTree = sample.getSample(T[i], tmap, newTmap, subsampleSize, unique2Dup);
+
                 //call new weighted function
                 vector<double> iterData; iterData.resize(numComp,0);
                 Weighted thisWeighted(includeRoot);
@@ -660,7 +665,7 @@ int UnifracWeightedCommand::runRandomCalcs(Tree* thisTree, vector<double> usersS
                 createProcesses(thisTree,  namesOfGroupCombos, rScores);
             }
 #else
-            driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
+            driver(thisTree, namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
 #endif
             
             if (m->control_pressed) { delete tmap;  for (int i = 0; i < T.size(); i++) { delete T[i]; } delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } return 0; }