added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 89ab0a49a7592a86638d801aaaf0257f63a34379..e0d62dd5ddd7acd106d18af31de013f6fce9c462 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -280,13 +280,13 @@ CollectCommand::CollectCommand(string option)  {
 
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
-                       convert(temp, freq); 
+                       m->mothurConvert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
-                       convert(temp, abund); 
+                       m->mothurConvert(temp, abund); 
                        
                        temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
-                       convert(temp, size); 
+                       m->mothurConvert(temp, size); 
                }
                
        }
@@ -307,7 +307,7 @@ int CollectCommand::execute(){
        
                for (int p = 0; p < inputFileNames.size(); p++) {
                        
-                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  m->Groups.clear();  return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  m->clearGroups();  return 0; }
                        
                        if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
                        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
@@ -416,7 +416,7 @@ int CollectCommand::execute(){
                                for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear(); 
                                delete input;  
                                delete order; 
-                               m->Groups.clear();
+                               m->clearGroups();
                                return 0;
                        }
 
@@ -428,7 +428,7 @@ int CollectCommand::execute(){
                                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear(); 
                                        delete input;  
                                        delete order; 
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
 
@@ -476,7 +476,7 @@ int CollectCommand::execute(){
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
                                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear(); 
                                        delete input;  
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                        }
                                
@@ -509,7 +509,7 @@ int CollectCommand::execute(){
                                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear(); 
                                        delete input;  
                                        delete order;
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
                                delete order;