-//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