added multiple processors option for Windows users to align.seqs, dist.seqs, summary...

[mothur.git] / getgroupscommand.cpp

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index d3470f16ad990d7285e51e534ad059666a03d097..5021f4085534cfc84a17d5875e449cf90f9f1d53 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -203,7 +203,7 @@ GetGroupsCommand::GetGroupsCommand(string option)  {
                        if (groups == "not found") { groups = ""; }
                        else {
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
@@ -273,7 +273,9 @@ int GetGroupsCommand::execute(){
                        //make sure groups are valid
                        //takes care of user setting groupNames that are invalid or setting groups=all
                        SharedUtil* util = new SharedUtil();
-                       util->setGroups(Groups, groupMap->namesOfGroups);
+                       vector<string> gNamesOfGroups = groupMap->getNamesOfGroups();
+                       util->setGroups(Groups, gNamesOfGroups);
+                       groupMap->setNamesOfGroups(gNamesOfGroups);
                        delete util;
                        
                        //fill names with names of sequences that are from the groups we want to remove 
@@ -711,7 +713,7 @@ void GetGroupsCommand::readAccnos(){
                }
                in.close();             
                
-               m->Groups = Groups;
+               m->setGroups(Groups);
                
        }
        catch(exception& e) {