changed all shared commands so that they read the shared file generated by the read...

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 047ea6173103b5c2ad82c19c6213ab5bab9ed978..ac82da5e558d2965829de82f170b1514c8972c84 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -88,23 +88,13 @@ int TreeGroupCommand::execute(){
                //if the users entered no valid calculators don't execute command
                if (treeCalculators.size() == 0) { return 0; }
 
-               if (format == "sharedfile") {
-                       //you have groups
-                       read = new ReadOTUFile(globaldata->inputFileName);      
-                       read->read(&*globaldata); 
+               //you have groups
+               read = new ReadOTUFile(globaldata->inputFileName);      
+               read->read(&*globaldata); 
                        
-                       input = globaldata->ginput;
-                       lookup = input->getSharedRAbundVectors();
-               }else {
-                       //you are using a list and a groupfile
-                       read = new ReadOTUFile(globaldata->inputFileName);      
-                       read->read(&*globaldata); 
-               
-                       input = globaldata->ginput;
-                       SharedList = globaldata->gSharedList;
-                       lookup = SharedList->getSharedRAbundVector();
-               }
-               
+               input = globaldata->ginput;
+               lookup = input->getSharedRAbundVectors();
+                               
                if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; }
                
                numGroups = globaldata->Groups.size();