added warning about average neighbor merges around cutoff. fixed little bugs.

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index baf4224c952a5a47bea7aa911f56196c6dabdead..93ba1f9b65b8146b666d32debb3df601c046b19a 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -81,9 +81,9 @@ ClusterCommand::ClusterCommand(string option){
                                }
                                
                                //create cluster
-                               if (method == "furthest")       {       cluster = new CompleteLinkage(rabund, list, matrix); }
-                               else if(method == "nearest"){   cluster = new SingleLinkage(rabund, list, matrix); }
-                               else if(method == "average"){   cluster = new AverageLinkage(rabund, list, matrix);     }
+                               if (method == "furthest")       {       cluster = new CompleteLinkage(rabund, list, matrix, cutoff); }
+                               else if(method == "nearest"){   cluster = new SingleLinkage(rabund, list, matrix, cutoff); }
+                               else if(method == "average"){   cluster = new AverageLinkage(rabund, list, matrix, cutoff);     }
                                tag = cluster->getTag();
 
                                fileroot = getRootName(globaldata->inputFileName);