X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.cpp;h=96662bc36d4b77e1cb8b7a884f4e8460969033f4;hb=f12174bc43f9e8ad536f2a37fb3a763b1ac90ba9;hp=a1e787bab8cd24ebb352593055e7d2fc10b406de;hpb=01f6af90c907264686304a5c684c702e94ff40ae;p=mothur.git

diff --git a/sequence.cpp b/sequence.cpp
index a1e787b..96662bc 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -300,7 +300,7 @@ string Sequence::getSequenceString(ifstream& fastaFile, int& numAmbig) {
 			if(letter == '>'){
 				fastaFile.putback(letter);
 				break;
-			}
+			}else if (letter == ' ') {;}
 			else if(isprint(letter)){
 				letter = toupper(letter);
 				if(letter == 'U'){letter = 'T';}
@@ -354,7 +354,7 @@ string Sequence::getSequenceString(istringstream& fastaFile, int& numAmbig) {
 			if(letter == '>'){
 				fastaFile.putback(letter);
 				break;
-			}
+			}else if (letter == ' ') {;}
 			else if(isprint(letter)){
 				letter = toupper(letter);
 				if(letter == 'U'){letter = 'T';}
@@ -682,7 +682,7 @@ int Sequence::getEndPos(){
 //********************************************************************************************************************
 
 void Sequence::padFromPos(int end){
-	cout << end << '\t' << endPos << endl;
+	//cout << end << '\t' << endPos << endl;
 	for(int j = end; j < endPos; j++) {
 		aligned[j] = '.';
 	}