added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index 4c6c6d8c8f0d628653ff772a367b07cdbadecced..3bf0d572f88d0ad7ffd76989d71f10807e8cc659 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -47,7 +47,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                }
                        }
                        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, "", threadID);     }
                        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.");
@@ -89,7 +89,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                        m->mothurOut("Generating search database...    "); cout.flush();
        #ifdef USE_MPI  
                                int pid, processors;
-                               vector<unsigned long int> positions;
+                               vector<unsigned long long> positions;
                                int tag = 2001;
                        
                                MPI_Status status; 
@@ -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();
@@ -176,7 +176,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                }
                        }
                        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, "", threadID);     }
                        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.");
@@ -238,7 +238,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
        }
 }
 /**************************************************************************************************/
-Classify::Classify() {         m = MothurOut::getInstance();   database = NULL;        }
+Classify::Classify() {         m = MothurOut::getInstance();   database = NULL;        flipped=false; }
 /**************************************************************************************************/
 
 int Classify::readTaxonomy(string file) {
@@ -252,7 +252,7 @@ int Classify::readTaxonomy(string file) {
 
 #ifdef USE_MPI 
                int pid, num, processors;
-               vector<unsigned long int> positions;
+               vector<unsigned long long> positions;
                int tag = 2001;
                
                MPI_Status status;