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

[mothur.git] / clusterdoturcommand.cpp

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 3f629dc09af39d7c9785a18687d9aecb8bee5f58..603bd73d680b485fb4df6ef6cf62e935af3f1ff5 100644 (file)
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -146,11 +146,11 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                        if (temp == "not found") { temp = "100"; }
                        //saves precision legnth for formatting below
                        length = temp.length();
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));  
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
@@ -219,7 +219,7 @@ int ClusterDoturCommand::execute(){
                int estart = time(NULL);
        
                while ((cluster->getSmallDist() < cutoff) && (cluster->getNSeqs() > 1)){
-                       if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close();  for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());         } outputTypes.clear();  return 0;  }
+                       if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close();  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);        } outputTypes.clear();  return 0;  }
                
                        cluster->update(cutoff);