else if(isprint(letter)){
letter = toupper(letter);
if(letter == 'U'){letter = 'T';}
+ if(letter != '.' && letter != '-' && letter != 'A' && letter != 'T' && letter != 'G' && letter != 'C'){
+ letter = 'N';
+ }
sequence += letter;
}
}
else { return aligned; }
}
+//********************************************************************************************************************
+
+string Sequence::getInlineSeq(){
+ return name + '\t' + aligned;
+}
+
+
//********************************************************************************************************************
string Sequence::getPairwise(){
//********************************************************************************************************************
int Sequence::getStartPos(){
- if(endPos == -1){
+ if(startPos == -1){
for(int j = 0; j < alignmentLength; j++) {
if(aligned[j] != '.'){
startPos = j + 1;
//********************************************************************************************************************
+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--){
//********************************************************************************************************************
+void Sequence::padFromPos(int end){
+
+ for(int j = end; j < endPos; j++) {
+ aligned[j] = '.';
+ }
+ endPos = end;
+
+}
+
+//********************************************************************************************************************
+
bool Sequence::getIsAligned(){
return isAligned;
}