1.22.0

[mothur.git] / heatmapsimcommand.cpp

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 38e344dfea67fdcfe89ce80a0476300d8ff50e3a..1b6fc5bc427f48e68171f47654b18363afc21e9e 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -234,7 +234,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                        if (groups == "not found") { groups = ""; }
                        else { 
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                        
                        
@@ -294,7 +294,7 @@ int HeatMapSimCommand::execute(){
                
                delete heatmap;
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } outputTypes.clear(); return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } outputTypes.clear(); return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -325,12 +325,12 @@ int HeatMapSimCommand::runCommandShared() {
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) {  delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  m->Groups.clear(); return 0; }
+               if (m->control_pressed) {  delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  m->clearGroups(); return 0; }
                
                //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) { delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); return 0; }
+                       if (m->control_pressed) { delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); return 0; }
 
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
        
@@ -370,7 +370,7 @@ int HeatMapSimCommand::runCommandShared() {
                }
                
                        
-               if (m->control_pressed) {  delete input;  m->Groups.clear();  return 0; }
+               if (m->control_pressed) {  delete input;  m->clearGroups();  return 0; }
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -385,7 +385,7 @@ int HeatMapSimCommand::runCommandShared() {
                        }
                }
                
-               if (m->control_pressed) {  delete input;  m->Groups.clear(); return 0; }
+               if (m->control_pressed) {  delete input;  m->clearGroups(); return 0; }
                
                //run last label if you need to
                if (needToRun == true)  {
@@ -399,10 +399,10 @@ int HeatMapSimCommand::runCommandShared() {
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                }
                
-               if (m->control_pressed) {  delete input;  m->Groups.clear(); return 0; }
+               if (m->control_pressed) {  delete input;  m->clearGroups(); return 0; }
                        
                //reset groups parameter
-               m->Groups.clear();  
+               m->clearGroups();  
                        
                delete input;