fixed order of unifrac commands so that it matches the summary commands

[mothur.git] / consensuscommand.cpp

diff --git a/consensuscommand.cpp b/consensuscommand.cpp
index 37cd39578c953e3d843c4cd0892b1be992511a88..a65d56fb86c2a8a91ac2915def73d05c7e53b6d6 100644 (file)
--- a/consensuscommand.cpp
+++ b/consensuscommand.cpp
@@ -68,7 +68,7 @@ int ConcensusCommand::execute(){
                
                //open file for pairing not included in the tree
                notIncluded = filename + ".cons.pairs";
-               openOutputFile(notIncluded, out2);
+               m->openOutputFile(notIncluded, out2);
                
                consensusTree = new Tree();
                
@@ -151,7 +151,7 @@ int ConcensusCommand::execute(){
                }
                
                outputFile = filename + ".cons.tre";
-               openOutputFile(outputFile, out);
+               m->openOutputFile(outputFile, out);
                
                consensusTree->printForBoot(out);
                
@@ -262,13 +262,13 @@ int ConcensusCommand::getSets() {
                while (nodePairsCopy.size() != 0) {
                        if (m->control_pressed) { return 1; }
                
-                       vector<string> small = getSmallest(nodePairsCopy);
+                       vector<string> smallOne = getSmallest(nodePairsCopy);
                        
-                       int subgrouprate = getSubgroupRating(small);
+                       int subgrouprate = getSubgroupRating(smallOne);
                
-                       nodePairsInitialRate[small] = nodePairs[small] + subgrouprate;
+                       nodePairsInitialRate[smallOne] = nodePairs[smallOne] + subgrouprate;
                        
-                       nodePairsCopy.erase(small);
+                       nodePairsCopy.erase(smallOne);
                }
                
                return 0;