This is mothur v 1.2.0 - the April ~24, 2009 release

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 6cc64feed9cb3b031b87ed9ea92bad616a362621..e50fbaad53f0438a44bc25bf5b7c55fbf9146b83 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -17,6 +17,7 @@
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
 #include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
 
 
 //**********************************************************************************************************************
@@ -33,7 +34,7 @@ TreeGroupCommand::TreeGroupCommand(){
                        if (validCalculator->isValidCalculator("treegroup", globaldata->Estimators[i]) == true) { 
                                if (globaldata->Estimators[i] == "jabund") {    
                                        treeCalculators.push_back(new JAbund());
-                               }else if (globaldata->Estimators[i] == "sorensonabund") { 
+                               }else if (globaldata->Estimators[i] == "sorabund") { 
                                        treeCalculators.push_back(new SorAbund());
                                }else if (globaldata->Estimators[i] == "jclass") { 
                                        treeCalculators.push_back(new Jclass());
@@ -49,6 +50,8 @@ TreeGroupCommand::TreeGroupCommand(){
                                        treeCalculators.push_back(new ThetaN());
                                }else if (globaldata->Estimators[i] == "morisitahorn") { 
                                        treeCalculators.push_back(new MorHorn());
+                               }else if (globaldata->Estimators[i] == "braycurtis") { 
+                                       treeCalculators.push_back(new BrayCurtis());
                                }
                        }
                }
@@ -85,14 +88,14 @@ int TreeGroupCommand::execute(){
                if (treeCalculators.size() == 0) { return 0; }
 
                if (format == "sharedfile") {
-                       read = new ReadPhilFile(globaldata->inputFileName);     
+                       read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
                        
                        input = globaldata->ginput;
                        order = input->getSharedOrderVector();
                }else {
                        //you are using a list and a groupfile
-                       read = new ReadPhilFile(globaldata->inputFileName);     
+                       read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
                
                        input = globaldata->ginput;