1.23.0

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index ec2d8e003a31a712de8c32d255d164b6b13cd46c..16618f74cc8e251c7d28d10ca37fcd2e7b09d017 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -220,26 +220,26 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        string temp;
                        temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
-                       convert(temp, startPos); 
+                       m->mothurConvert(temp, startPos); 
                
                        temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
-                       convert(temp, endPos);  
+                       m->mothurConvert(temp, endPos);  
 
                        temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
-                       convert(temp, maxAmbig);  
+                       m->mothurConvert(temp, maxAmbig);  
 
                        temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
-                       convert(temp, maxHomoP);  
+                       m->mothurConvert(temp, maxHomoP);  
 
                        temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
-                       convert(temp, minLength); 
+                       m->mothurConvert(temp, minLength); 
                        
                        temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
-                       convert(temp, maxLength); 
+                       m->mothurConvert(temp, maxLength); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
                        if (temp == "not found"){       temp = "none";          }
@@ -259,7 +259,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
                        if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
                        
                        temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){       temp = "90";                            }
-                       convert(temp, criteria); 
+                       m->mothurConvert(temp, criteria); 
                }
 
        }