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

[mothur.git] / bootstrapsharedcommand.cpp

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index e88972cc19aae9c2e21efa665177925c3e86cf46..6b1f338661820d5f205556f9e62b347664e5cb4d 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -95,23 +95,13 @@ int BootSharedCommand::execute(){
        
                //if the users entered no valid calculators don't execute command
                if (treeCalculators.size() == 0) { return 0; }
-
-               if (format == "sharedfile") {
-                       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();
-               }
                
+               //read first line
+               read = new ReadOTUFile(globaldata->inputFileName);      
+               read->read(&*globaldata); 
+               input = globaldata->ginput;
+               order = input->getSharedOrderVector();
+                               
                //set users groups
                util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
                numGroups = globaldata->Groups.size();
@@ -186,17 +176,7 @@ int BootSharedCommand::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++;
                }