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

[mothur.git] / mergegroupscommand.cpp

diff --git a/mergegroupscommand.cpp b/mergegroupscommand.cpp
index 8df6b62c5a1ccd997b6147e0018063193436649e..af2af96b4dc6ae122fd0b9383d9486b3c776234e 100644 (file)
--- a/mergegroupscommand.cpp
+++ b/mergegroupscommand.cpp
@@ -150,7 +150,7 @@ MergeGroupsCommand::MergeGroupsCommand(string option) {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "all";  }
                        m->splitAtDash(groups, Groups);
-                       m->Groups = Groups;
+                       m->setGroups(Groups);
                }
                
        }
@@ -187,7 +187,7 @@ int MergeGroupsCommand::execute(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if (m->control_pressed) {  out.close(); for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); } return 0; }
+                       if (m->control_pressed) {  out.close(); for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]); } return 0; }
                        
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                
@@ -221,13 +221,13 @@ int MergeGroupsCommand::execute(){
                        //prevent memory leak
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
                        
-                       if (m->control_pressed) {  out.close(); m->Groups.clear();   delete designMap;  for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0; }
+                       if (m->control_pressed) {  out.close(); m->clearGroups();   delete designMap;  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); } return 0; }
                        
                        //get next line to process
                        lookup = input.getSharedRAbundVectors();                                
                }
                
-               if (m->control_pressed) { out.close(); m->Groups.clear();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]); }  return 0; }
+               if (m->control_pressed) { out.close(); m->clearGroups();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); }  return 0; }
                
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -257,7 +257,7 @@ int MergeGroupsCommand::execute(){
                
                out.close();
                //reset groups parameter
-               m->Groups.clear();  
+               m->clearGroups();  
                delete designMap;
                
                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0;}