added multiple processors option for Windows users to align.seqs, dist.seqs, summary...

[mothur.git] / alignmentdb.cpp

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 6ccfd39edf3562d6795db6c9de131287b86241e0..57975d6d774a97b1d171b468c7a238158a7b0ebe 100644 (file)
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -15,7 +15,7 @@
 
 /**************************************************************************************************/
 //deep copy
-AlignmentDB::AlignmentDB(const AlignmentDB& adb) : numSeqs(adb.numSeqs), longest(adb.longest), method(adb.method), emptySequence(adb.emptySequence) {
+AlignmentDB::AlignmentDB(const AlignmentDB& adb) : numSeqs(adb.numSeqs), longest(adb.longest), method(adb.method), emptySequence(adb.emptySequence), threadID(adb.threadID) {
        try {
                
                m = MothurOut::getInstance();
@@ -41,7 +41,7 @@ AlignmentDB::AlignmentDB(const AlignmentDB& adb) : numSeqs(adb.numSeqs), longest
        
 }
 /**************************************************************************************************/
-AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch){           //      This assumes that the template database is in fasta format, may 
+AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int tid){          //      This assumes that the template database is in fasta format, may 
        try {                                                                                   //      need to alter this in the future?
                m = MothurOut::getInstance();
                longest = 0;
@@ -49,6 +49,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                bool needToGenerate = true;
                ReferenceDB* rdb = ReferenceDB::getInstance();
                bool silent = false;
+               threadID = tid;
                
                if (fastaFileName == "saved-silent") {
                        fastaFileName = "saved"; silent = true;
@@ -189,7 +190,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                        #endif
                }
                else if(method == "suffix")             {       search = new SuffixDB(numSeqs);                                                         }
-               else if(method == "blast")              {       search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "");       }
+               else if(method == "blast")              {       search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID);     }
                else {
                        method = "kmer";
                        m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
@@ -231,7 +232,7 @@ AlignmentDB::AlignmentDB(string s){
                method = s;
                
                if(method == "suffix")          {       search = new SuffixDB();        }
-               else if(method == "blast")      {       search = new BlastDB("");               }
+               else if(method == "blast")      {       search = new BlastDB("", 0);            }
                else                                            {       search = new KmerDB();          }