X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.cpp;h=3bf0d572f88d0ad7ffd76989d71f10807e8cc659;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=eb0865c2744acfe120505a5a533cd482af8b9b19;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063;p=mothur.git

diff --git a/classify.cpp b/classify.cpp
index eb0865c..3bf0d57 100644
--- a/classify.cpp
+++ b/classify.cpp
@@ -123,7 +123,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 				//create database
 				if(method == "kmer")			{	database = new KmerDB(tempFile, kmerSize);			}
 				else if(method == "suffix")		{	database = new SuffixDB(numSeqs);								}
-				else if(method == "blast")		{	database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "");	}
+				else if(method == "blast")		{	database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", pid);	}
 				else if(method == "distance")	{	database = new DistanceDB();	}
 				else {
 					m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8."); m->mothurOutEndLine();
@@ -238,7 +238,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 	}
 }
 /**************************************************************************************************/
-Classify::Classify() {		m = MothurOut::getInstance();	database = NULL;	}
+Classify::Classify() {		m = MothurOut::getInstance();	database = NULL;	flipped=false; }
 /**************************************************************************************************/
 
 int Classify::readTaxonomy(string file) {