X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignmentdb.cpp;h=f59c5db7d6e6ef2d039ccdda8b48a6ea3fb6428a;hb=96dbe925073caefaed6e6db85659c144a806aeb1;hp=57975d6d774a97b1d171b468c7a238158a7b0ebe;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 57975d6..f59c5db 100644
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -13,33 +13,6 @@
 #include "blastdb.hpp"
 #include "referencedb.h"
 
-/**************************************************************************************************/
-//deep copy
-AlignmentDB::AlignmentDB(const AlignmentDB& adb) : numSeqs(adb.numSeqs), longest(adb.longest), method(adb.method), emptySequence(adb.emptySequence), threadID(adb.threadID) {
-	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, int tid){		//	This assumes that the template database is in fasta format, may 
 	try {											//	need to alter this in the future?
@@ -77,7 +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;