X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignmentdb.cpp;h=f59c5db7d6e6ef2d039ccdda8b48a6ea3fb6428a;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=6ccfd39edf3562d6795db6c9de131287b86241e0;hpb=d3aed959ca3b68890eeb7b815e24210bcfeb256c;p=mothur.git

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 6ccfd39..f59c5db 100644
--- 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();		}