X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.cpp;h=6aa0c0f8ae2c46a32edde8a67276ccb966bc0003;hb=0bcfddf7bc721a334bdae42d86a580019303537d;hp=872a0f091d49fddac359d528c53c799a50ef3c66;hpb=c67cf4168e1a124088b6f017946f0aa1fbdf1301;p=mothur.git

diff --git a/sequence.cpp b/sequence.cpp
index 872a0f0..6aa0c0f 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -427,6 +427,13 @@ string Sequence::getAligned(){
 	else				{  return aligned;  }
 }
 
+//********************************************************************************************************************
+
+string Sequence::getInlineSeq(){
+	return name + '\t' + aligned;	
+}
+
+
 //********************************************************************************************************************
 
 string Sequence::getPairwise(){
@@ -514,7 +521,7 @@ int Sequence::getLongHomoPolymer(){
 //********************************************************************************************************************
 
 int Sequence::getStartPos(){
-	if(endPos == -1){
+	if(startPos == -1){
 		for(int j = 0; j < alignmentLength; j++) {
 			if(aligned[j] != '.'){
 				startPos = j + 1;
@@ -529,6 +536,17 @@ int Sequence::getStartPos(){
 
 //********************************************************************************************************************
 
+void Sequence::padToPos(int start){
+
+	for(int j = startPos-1; j < start-1; j++) {
+		aligned[j] = '.';
+	}
+	startPos = start;
+
+}
+
+//********************************************************************************************************************
+
 int Sequence::getEndPos(){
 	if(endPos == -1){
 		for(int j=alignmentLength-1;j>=0;j--){
@@ -545,6 +563,17 @@ int Sequence::getEndPos(){
 
 //********************************************************************************************************************
 
+void Sequence::padFromPos(int end){
+	
+	for(int j = end; j < endPos; j++) {
+		aligned[j] = '.';
+	}
+	endPos = end;
+	
+}
+
+//********************************************************************************************************************
+
 bool Sequence::getIsAligned(){
 	return isAligned;
 }