X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignmentdb.cpp;h=5c758ecebb249710be141813a734eb571b88da32;hb=df92022fc75c08b91cefa2c6ca4fd7b23eb480b0;hp=6b05989d40a0184540a9397fb75efd79e49a14cc;hpb=ef3f6d42fe720cd6d91419e5e32f8c04d8765010;p=mothur.git

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 6b05989..5c758ec 100644
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -17,7 +17,7 @@
 AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch){		//	This assumes that the template database is in fasta format, may 
 	try {											//	need to alter this in the future?
 		longest = 0;
-		
+
 		ifstream fastaFile;
 		openInputFile(fastaFileName, fastaFile);
 		
@@ -25,14 +25,13 @@ AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, floa
 		mothurOut("Reading in the " + fastaFileName + " template sequences...\t");	cout.flush();
 		
 		while (!fastaFile.eof()) {
-			Sequence temp(fastaFile);
-			
-			templateSequences.push_back(temp);
+			Sequence temp(fastaFile);  gobble(fastaFile);
 			
-			//save longest base
-			if (temp.getUnaligned().length() > longest)  { longest = temp.getUnaligned().length(); }
-			
-			gobble(fastaFile);
+			if (temp.getName() != "") {
+				templateSequences.push_back(temp);
+				//save longest base
+				if (temp.getUnaligned().length() > longest)  { longest = temp.getUnaligned().length()+1; }
+			}
 		}
 		
 		numSeqs = templateSequences.size();