1.23.0

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index ef23375df9425f11816acbf8594f46e613e9e148..00f960bbbab8d07ecbee08dc01b78907c60c0185 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -144,7 +144,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "-1"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; allLines = 1; }
@@ -215,7 +215,7 @@ int PhylotypeCommand::execute(){
                        
                        if (m->control_pressed) { 
                                outRabund.close(); outSabund.close(); outList.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
                                delete tree; return 0; 
                        }
                        
@@ -286,7 +286,7 @@ int PhylotypeCommand::execute(){
                delete tree;
                
                if (m->control_pressed) { 
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
                        return 0; 
                }