X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.cpp;h=96662bc36d4b77e1cb8b7a884f4e8460969033f4;hb=55bbd10379db27def51cec72a8819d775f73e45b;hp=d877f4b93f33d8123ff6a1a9f7f839dc680fcf61;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/sequence.cpp b/sequence.cpp
index d877f4b..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';}
@@ -603,7 +603,7 @@ int Sequence::getLongHomoPolymer(){
 int Sequence::getStartPos(){
 	if(startPos == -1){
 		for(int j = 0; j < alignmentLength; j++) {
-			if(aligned[j] != '.'){
+			if((aligned[j] != '.')&&(aligned[j] != '-')){
 				startPos = j + 1;
 				break;
 			}
@@ -668,7 +668,7 @@ int Sequence::filterFromPos(int end){
 int Sequence::getEndPos(){
 	if(endPos == -1){
 		for(int j=alignmentLength-1;j>=0;j--){
-			if(aligned[j] != '.'){
+			if((aligned[j] != '.')&&(aligned[j] != '-')){
 				endPos = j + 1;
 				break;
 			}
@@ -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] = '.';
 	}