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

[mothur.git] / removegroupscommand.cpp

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 252a92573d036c47f4d45235113adef1fc44727a..81722dd3e4047fc2505d64372a2ca539978c9445 100644 (file)
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -204,7 +204,7 @@ RemoveGroupsCommand::RemoveGroupsCommand(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 +273,8 @@ int RemoveGroupsCommand::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> namesGroups = groupMap->getNamesOfGroups();
+                       util->setGroups(Groups, namesGroups);
                        delete util;
                        
                        //fill names with names of sequences that are from the groups we want to remove 
@@ -403,23 +404,23 @@ int RemoveGroupsCommand::readShared(){
                vector<SharedRAbundVector*> lookup = tempInput->getSharedRAbundVectors();
        
                //save m->Groups
-               vector<string> allGroupsNames = m->namesOfGroups;
-               vector<string> mothurOutGroups = m->Groups;
+               vector<string> allGroupsNames = m->getAllGroups();
+               vector<string> mothurOutGroups = m->getGroups();
                
                vector<string> groupsToKeep;
                for (int i = 0; i < allGroupsNames.size(); i++) {
-                       if (!m->inUsersGroups(allGroupsNames[i], m->Groups)) {
+                       if (!m->inUsersGroups(allGroupsNames[i], m->getGroups())) {
                                groupsToKeep.push_back(allGroupsNames[i]);
                        }
                }
                
-               if (allGroupsNames.size() == groupsToKeep.size()) { m->mothurOut("Your file does not contain any groups you wish to remove."); m->mothurOutEndLine(); m->Groups = mothurOutGroups; delete tempInput; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  return 0; }
+               if (allGroupsNames.size() == groupsToKeep.size()) { m->mothurOut("Your file does not contain any groups you wish to remove."); m->mothurOutEndLine(); m->setGroups(mothurOutGroups); delete tempInput; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  return 0; }
                
                //reset read 
                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                delete tempInput;
-               m->Groups = groupsToKeep;
-               m->namesOfGroups.clear();
+               m->setGroups(groupsToKeep);
+               m->clearAllGroups();
                m->names.clear();
                m->saveNextLabel = "";
                m->printedHeaders = false;
@@ -458,7 +459,7 @@ int RemoveGroupsCommand::readShared(){
                }
                
                
-               m->Groups = mothurOutGroups;
+               m->setGroups(mothurOutGroups);
                
                if (wroteSomething == false) {  m->mothurOut("Your file contains only the groups you wish to remove."); m->mothurOutEndLine();  }
                
@@ -745,7 +746,7 @@ void RemoveGroupsCommand::readAccnos(){
                }
                in.close();     
                
-               m->Groups = Groups;
+               m->setGroups(Groups);
                
        }
        catch(exception& e) {