1.23.0

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index af6d91449065af894f086c497cfcbc171f374098..9ee7b5e946a7f5819cbac94bab7efe8c0cb71aef 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -374,19 +374,14 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        string temp;
                        temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
-                       convert(temp, kmerSize); 
+                       m->mothurConvert(temp, kmerSize); 
                        
                        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, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
-                       //this is so the threads can quickly load the reference data
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                       #else
-                       if ((processors != 1) && (rdb->referenceSeqs.size() == 0)) { save = true; }
-                       #endif
                        rdb->save = save; 
                        if (save) { //clear out old references
                                rdb->clearMemory();     
@@ -425,28 +420,28 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "bayesian";    }
                        
                        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, "numwanted", false);        if (temp == "not found"){       temp = "10";                    }
-                       convert(temp, numWanted);
+                       m->mothurConvert(temp, numWanted);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found"){       temp = "0";                             }
-                       convert(temp, cutoff);
+                       m->mothurConvert(temp, cutoff);
                        
                        temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
                        probs = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "iters", false);            if (temp == "not found") { temp = "100";                        }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters);