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

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 02461365b505bdea22cc977594fc1341ca7bac46..2312649d1cff739956638ba2ad8788949669f1d5 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -182,7 +182,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                        else { 
                                userGroups = "unique." + groups;
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                                
                        }
                        
@@ -191,7 +191,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                        else { 
                                userGroups = groups;
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                                unique = false;
                        }
                        
@@ -221,7 +221,7 @@ int GetSharedOTUCommand::execute(){
                if (m->control_pressed) { delete groupMap; return 0; }
                
                if (Groups.size() == 0) {
-                       Groups = groupMap->namesOfGroups;
+                       Groups = groupMap->getNamesOfGroups();
                        
                        //make string for outputfile name
                        userGroups = "unique.";
@@ -230,7 +230,9 @@ int GetSharedOTUCommand::execute(){
                }else{
                        //sanity check for group names
                        SharedUtil util;
-                       util.setGroups(Groups, groupMap->namesOfGroups);
+                       vector<string> namesOfGroups = groupMap->getNamesOfGroups(); 
+                       util.setGroups(Groups, namesOfGroups);
+                       groupMap->setNamesOfGroups(namesOfGroups);
                }
        
                //put groups in map to find easier
@@ -325,7 +327,7 @@ int GetSharedOTUCommand::execute(){
                
 
                //reset groups parameter
-               m->Groups.clear();  
+               m->clearGroups();  
                
                if (lastlist != NULL) {         delete lastlist;        }