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

[mothur.git] / normalizesharedcommand.cpp

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 51c755cc6bdc91d767e56c79771bfe1d81fef2c4..bcec00a0bc6dd47e15ddcf72000dc4a9dbec9469 100644 (file)
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -166,7 +166,7 @@ NormalizeSharedCommand::NormalizeSharedCommand(string option) {
                        else { 
                                pickedGroups = true;
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                        
                        method = validParameter.validFile(parameters, "method", false);                         if (method == "not found") { method = "totalgroup"; }
@@ -206,18 +206,20 @@ int NormalizeSharedCommand::execute(){
                        
                        //look for groups whose numseqs is below norm and remove them, warning the user
                        if (norm != 0) { 
-                               m->Groups.clear();
+                               m->clearGroups();
+                               vector<string> mGroups;
                                vector<SharedRAbundVector*> temp;
                                for (int i = 0; i < lookup.size(); i++) {
                                        if (lookup[i]->getNumSeqs() < norm) { 
                                                m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
                                                delete lookup[i];
                                        }else { 
-                                               m->Groups.push_back(lookup[i]->getGroup()); 
+                                               mGroups.push_back(lookup[i]->getGroup()); 
                                                temp.push_back(lookup[i]);
                                        }
                                } 
                                lookup = temp;
+                               m->setGroups(mGroups);
                        }
                        
                        //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
@@ -240,7 +242,7 @@ int NormalizeSharedCommand::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) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear();   return 0; }
+                               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups();   return 0; }
                                
                                if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                        
@@ -271,13 +273,13 @@ int NormalizeSharedCommand::execute(){
                                //prevent memory leak
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
                                
-                               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } outputTypes.clear(); m->Groups.clear();  return 0; }
+                               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } outputTypes.clear(); m->clearGroups();  return 0; }
                                
                                //get next line to process
                                lookup = input->getSharedRAbundVectors();                               
                        }
                        
-                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear(); m->Groups.clear();   return 0; }
+                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear(); m->clearGroups();   return 0; }
                        
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -314,18 +316,20 @@ int NormalizeSharedCommand::execute(){
                        
                        //look for groups whose numseqs is below norm and remove them, warning the user
                        if (norm != 0) { 
-                               m->Groups.clear();
+                               m->clearGroups();
+                               vector<string> mGroups;
                                vector<SharedRAbundFloatVector*> temp;
                                for (int i = 0; i < lookupFloat.size(); i++) {
                                        if (lookupFloat[i]->getNumSeqs() < norm) { 
                                                m->mothurOut(lookupFloat[i]->getGroup() + " contains " + toString(lookupFloat[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
                                                delete lookupFloat[i];
                                        }else { 
-                                               m->Groups.push_back(lookupFloat[i]->getGroup()); 
+                                               mGroups.push_back(lookupFloat[i]->getGroup()); 
                                                temp.push_back(lookupFloat[i]);
                                        }
                                } 
                                lookupFloat = temp;
+                               m->setGroups(mGroups);
                        }
                        
                        //set norm to smallest group number
@@ -343,7 +347,7 @@ int NormalizeSharedCommand::execute(){
                        //as long as you are not at the end of the file or done wih the lines you want
                        while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                                
-                               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear();  for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } m->Groups.clear();  return 0; }
+                               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear();  for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } m->clearGroups();  return 0; }
                                
                                if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){                     
                                        
@@ -376,13 +380,13 @@ int NormalizeSharedCommand::execute(){
                                //prevent memory leak
                                for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i]; lookupFloat[i] = NULL; }
                                
-                               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } outputTypes.clear(); m->Groups.clear();   return 0; }
+                               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } outputTypes.clear(); m->clearGroups();   return 0; }
                                
                                //get next line to process
                                lookupFloat = input->getSharedRAbundFloatVectors();                             
                        }
                        
-                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear(); m->Groups.clear();   return 0; }
+                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear(); m->clearGroups();   return 0; }
                        
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -411,7 +415,7 @@ int NormalizeSharedCommand::execute(){
                        
                }
                //reset groups parameter
-               m->Groups.clear();  
+               m->clearGroups();  
                delete input;
                
                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear(); return 0;}