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

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 89cf4e2732af38c6fff844490effde5f8676e76c..29dd50e749dfa097d8ac16ac6181e58c559833a8 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -68,22 +68,12 @@ int RareFactSharedCommand::execute(){
                //if the users entered no valid calculators don't execute command
                if (rDisplays.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;
-                       SharedList = globaldata->gSharedList;
-                       order = SharedList->getSharedOrderVector();
-               }
-               
+               input = globaldata->ginput;
+               order = input->getSharedOrderVector();
+                               
                //set users groups
                util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "rarefact");
                
@@ -102,18 +92,7 @@ int RareFactSharedCommand::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++;
                }