1.23.0

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 2245ac9a80a1ccd94b7f13273fb80f4ab6f004b7..114f545aa26eb326f078b6ab7e1b18e024ecdcb5 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -212,23 +212,23 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        string temp;
                        temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
-                       convert(temp, match);  
+                       m->mothurConvert(temp, match);  
                        
                        temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
-                       convert(temp, misMatch);  
+                       m->mothurConvert(temp, misMatch);  
                        
                        temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
-                       convert(temp, gapOpen);  
+                       m->mothurConvert(temp, gapOpen);  
                        
                        temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
-                       convert(temp, gapExtend); 
+                       m->mothurConvert(temp, gapExtend); 
                        
                        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, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
                        countends = m->isTrue(temp);