1.23.0

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 960d70229a084923fd1cc8dc368ff4b71d815cbd..f03a9017d4867f1d8634a0ef72a25f1590bf13b6 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -224,34 +224,29 @@ AlignCommand::AlignCommand(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, "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, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
                        flip = m->isTrue(temp); 
                        
                        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) { save = true; }
-                       #endif
                        rdb->save = save; 
                        if (save) { //clear out old references
                                rdb->clearMemory();
@@ -272,7 +267,7 @@ AlignCommand::AlignCommand(string option)  {
                        else {  if (save) {     rdb->setSavedReference(templateFileName);       }       }
                        
                        temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
-                       convert(temp, threshold); 
+                       m->mothurConvert(temp, threshold); 
                        
                        search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
                        if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
@@ -923,7 +918,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                        string extension = "";
                        if (i != 0) { extension = toString(i) + ".temp"; }
                        
-                       alignData* tempalign = new alignData((alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
+                       alignData* tempalign = new alignData(templateFileName, (alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
                        pDataArray.push_back(tempalign);
                        processIDS.push_back(i);