1.23.0

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index eb0865c2744acfe120505a5a533cd482af8b9b19..c92d9fdc6526788df19d9e6f487ffb641bbaca44 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -61,7 +61,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                        names.push_back(temp.getName());
                                        database->addSequence(temp);    
                                }
-                               database->generateDB();
+//                             database->generateDB();
                        }else if ((method == "kmer") && (!needToGenerate)) {    
                                ifstream kmerFileTest(kmerDBName.c_str());
                                database->readKmerDB(kmerFileTest);     
@@ -123,7 +123,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                //create database
                                if(method == "kmer")                    {       database = new KmerDB(tempFile, kmerSize);                      }
                                else if(method == "suffix")             {       database = new SuffixDB(numSeqs);                                                               }
-                               else if(method == "blast")              {       database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "");       }
+                               else if(method == "blast")              {       database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", pid);  }
                                else if(method == "distance")   {       database = new DistanceDB();    }
                                else {
                                        m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8."); m->mothurOutEndLine();
@@ -150,7 +150,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                        }
                                }
                                
-                               database->generateDB();
+//                             database->generateDB();
                                MPI_File_close(&inMPI);
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                #else
@@ -200,7 +200,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                }
                                fastaFile.close();
 
-                               database->generateDB();
+//                             database->generateDB();
                                
                        }else if ((method == "kmer") && (!needToGenerate)) {    
                                ifstream kmerFileTest(kmerDBName.c_str());
@@ -223,9 +223,9 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                        database->setNumSeqs(names.size());
                        
                        //sanity check
-                       bool okay = phyloTree->ErrorCheck(names);
+                       //bool okay = phyloTree->ErrorCheck(names);
                        
-                       if (!okay) { m->control_pressed = true; }
+                       //if (!okay) { m->control_pressed = true; }
                        
                        m->mothurOut("DONE."); m->mothurOutEndLine();
                        m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();