while(fastaFile){
letter=fastaFile.get();
if((letter == '\r') || (letter == '\n')){
- gobble(fastaFile); //in case its a \r\n situation
+ m->gobble(fastaFile); //in case its a \r\n situation
break;
}
}
while(fastaFile){
letter=fastaFile.get();
if((letter == '\r') || (letter == '\n')){
- gobble(fastaFile); //in case its a \r\n situation
+ m->gobble(fastaFile); //in case its a \r\n situation
break;
}
}
//********************************************************************************************************************
+void Sequence::removeAmbigBases(){
+
+ for(int j=0;j<alignmentLength;j++){
+ if(aligned[j] != 'A' && aligned[j] != 'T' && aligned[j] != 'G' && aligned[j] != 'C'){
+ aligned[j] = '-';
+ }
+ }
+ setUnaligned(aligned);
+}
+
+//********************************************************************************************************************
+
int Sequence::getLongHomoPolymer(){
if(longHomoPolymer == -1){
longHomoPolymer = 1;