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

[mothur.git] / countgroupscommand.cpp

diff --git a/countgroupscommand.cpp b/countgroupscommand.cpp
index af9993c8ef6f8ee794be8bf7b3825aa34d1a44e7..24b4214dd5600ef0f0625ba7acf0da2a8f328108 100644 (file)
--- a/countgroupscommand.cpp
+++ b/countgroupscommand.cpp
@@ -127,7 +127,7 @@ CountGroupsCommand::CountGroupsCommand(string option)  {
                        if (groups == "not found") { groups = ""; }
                        else {
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
@@ -153,7 +153,7 @@ CountGroupsCommand::CountGroupsCommand(string option)  {
                                }
                        }
                        
-                       if ((accnosfile == "") && (Groups.size() == 0)) { Groups.push_back("all"); m->Groups = Groups; }
+                       if ((accnosfile == "") && (Groups.size() == 0)) { Groups.push_back("all"); m->setGroups(Groups); }
                }
                
        }
@@ -179,7 +179,8 @@ int CountGroupsCommand::execute(){
                        //make sure groups are valid
                        //takes care of user setting groupNames that are invalid or setting groups=all
                        SharedUtil util;
-                       util.setGroups(Groups, groupMap.namesOfGroups);
+                       vector<string> nameGroups = groupMap.getNamesOfGroups();
+                       util.setGroups(Groups, nameGroups);
                        
                        for (int i = 0; i < Groups.size(); i++) {
                                m->mothurOut(Groups[i] + " contains " + toString(groupMap.getNumSeqs(Groups[i])) + "."); m->mothurOutEndLine();
@@ -224,7 +225,7 @@ void CountGroupsCommand::readAccnos(){
                }
                in.close();             
                
-               m->Groups = Groups;
+               m->setGroups(Groups);
                
        }
        catch(exception& e) {