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

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 96e495a58f9dd1bdc58256baf1ae47c51a9c87b2..86b35a5191d268452d86a2994dd1bcafd06a3001 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -129,21 +129,12 @@ int CollectSharedCommand::execute(){
                //if the users entered no valid calculators don't execute command
                if (cDisplays.size() == 0) { return 0; }
                
-               if (format == "sharedfile") {
-                       read = new ReadOTUFile(globaldata->inputFileName);      
-                       read->read(&*globaldata); 
+               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 ReadOTUFile(globaldata->inputFileName);      
-                       read->read(&*globaldata); 
+               input = globaldata->ginput;
+               order = input->getSharedOrderVector();
                
-                       input = globaldata->ginput;
-                       SharedList = globaldata->gSharedList;
-                       order = SharedList->getSharedOrderVector();
-               }
                set<string> orderList;
                
                //set users groups
@@ -164,18 +155,7 @@ int CollectSharedCommand::execute(){
                        }
                        
                        //get next line to process
-                       if (format == "sharedfile") {
-                               order = input->getSharedOrderVector();
-                       }else {
-                               //you are using a list and a groupfile
-                               SharedList = input->getSharedListVector(); //get new list vector to process
-                               if (SharedList != NULL) {
-                                       order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
-                               }else {
-                                       break;
-                               }
-                       }
-                       
+                       order = input->getSharedOrderVector();
                        count++;
                }
                set<string>::iterator i;