added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / alignmentdb.cpp

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 6ccfd39edf3562d6795db6c9de131287b86241e0..f59c5db7d6e6ef2d039ccdda8b48a6ea3fb6428a 100644 (file)
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -14,34 +14,7 @@
 #include "referencedb.h"
 
 /**************************************************************************************************/
-//deep copy
-AlignmentDB::AlignmentDB(const AlignmentDB& adb) : numSeqs(adb.numSeqs), longest(adb.longest), method(adb.method), emptySequence(adb.emptySequence) {
-       try {
-               
-               m = MothurOut::getInstance();
-               if (adb.method == "blast") {
-                       search = new BlastDB(*((BlastDB*)adb.search));
-               }else if(adb.method == "kmer") {
-                       search = new KmerDB(*((KmerDB*)adb.search));
-               }else if(adb.method == "suffix") {
-                       search = new SuffixDB(*((SuffixDB*)adb.search));
-               }else {
-                       m->mothurOut("[ERROR]: cannot create copy of alignment database, unrecognized method - " + adb.method); m->mothurOutEndLine();
-               }
-               
-               for (int i = 0; i < adb.templateSequences.size(); i++) {
-                       Sequence temp(adb.templateSequences[i]);
-                       templateSequences.push_back(temp);
-               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "AlignmentDB", "AlignmentDB");
-               exit(1);
-       }
-       
-}
-/**************************************************************************************************/
-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 +22,7 @@ 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;
@@ -76,7 +50,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                        
                        #ifdef USE_MPI  
                                int pid, processors;
-                               vector<unsigned long int> positions;
+                               vector<unsigned long long> positions;
                        
                                MPI_Status status; 
                                MPI_File inMPI;
@@ -189,7 +163,7 @@ 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 +205,7 @@ 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();          }