From: westcott <westcott>
Date: Wed, 18 Feb 2009 15:34:00 +0000 (+0000)
Subject: fixed bug in fastmap readFastaFile so that if there is a blank line inbetween the... 
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=46379d9bce0f4ba9433689d4828ef5a4aa78dfb5

fixed bug in fastmap readFastaFile so that if there is a blank line inbetween the sequences it still runs.
---

diff --git a/fastamap.cpp b/fastamap.cpp
index 1406523..1fefdd1 100644
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -20,22 +20,24 @@ void FastaMap::readFastaFile(ifstream& in) {
 	
 		//read through file
 		while (getline(in, line)) {
-			if (isalnum(line.at(0))){  //if it's a sequence line
-				sequence += line;
-			}
-			else{
+			if (line != "") {
+				if (isalnum(line.at(0))) {  //if it's a sequence line
+					sequence += line;
+				}
+				else{
 				//input sequence info into map
-				it = data.find(sequence);
-				if (it == data.end()) { 	//it's unique.
-					data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
-					data[sequence].groupnumber = 1;
-					data[sequence].names = name;
-				}else { // its a duplicate.
-					data[sequence].names += "," + name;
-					data[sequence].groupnumber++;
+					it = data.find(sequence);
+					if (it == data.end()) { 	//it's unique.
+						data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
+						data[sequence].groupnumber = 1;
+						data[sequence].names = name;
+					}else { // its a duplicate.
+						data[sequence].names += "," + name;
+						data[sequence].groupnumber++;
+					}
+					name = (line.substr(1, (line.npos))); //The line you just read is a new name so rip off '>'
+					sequence = "";
 				}
-				name = (line.substr(1, (line.npos))); //The line you just read is a new name so rip off '>'
-				sequence = "";
 			}
 		}