added concensus command and updated calcs

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index e50fbaad53f0438a44bc25bf5b7c55fbf9146b83..de30d3c5ac2e30ab6e44cb0f84cdb9e47c1eaf73 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -83,7 +83,8 @@ int TreeGroupCommand::execute(){
        try {
                int count = 1;  
                EstOutput data;
-       
+               vector<SharedRAbundVector*> subset;
+               
                //if the users entered no valid calculators don't execute command
                if (treeCalculators.size() == 0) { return 0; }
 
@@ -150,7 +151,12 @@ int TreeGroupCommand::execute(){
                                                for (int l = k; l < lookup.size(); l++) {
                                                        if (k != l) { //we dont need to similiarity of a groups to itself
                                                                //get estimated similarity between 2 groups
-                                                               data = treeCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
+                                                               
+                                                               subset.clear(); //clear out old pair of sharedrabunds
+                                                               //add new pair of sharedrabunds
+                                                               subset.push_back(lookup[k]); subset.push_back(lookup[l]); 
+                                                               
+                                                               data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
                                                                //save values in similarity matrix
                                                                simMatrix[k][l] = data[0];
                                                                simMatrix[l][k] = data[0];