public boolean hasUnalignedCharAt(int col){
  if (col < getFirstNonGapPosition()) {
    int firstUnalignedPrefixPos=getFirstNonGapPosition() - unalignedPrefix.length();
    if (col > firstUnalignedPrefixPos)     return true;
  }
 else   if (col >= getLastNonGapPosition()) {
    int lastUnalignedSuffixPos=getLastNonGapPosition() + unalignedSuffix.length();
    if (col < lastUnalignedSuffixPos)     return true;
  }
  return false;
}

public boolean hasUnalignedCharAt ( int col ) { if ( col < getFirstNonGapPosition ( ) ) { int firstUnalignedPrefixPos = getFirstNonGapPosition ( ) - unalignedPrefix . length ( ) ; if ( col > firstUnalignedPrefixPos ) return true ; } else if ( col >= getLastNonGapPosition ( ) ) { int lastUnalignedSuffixPos = getLastNonGapPosition ( ) + unalignedSuffix . length ( ) ; if ( col < lastUnalignedSuffixPos ) return true ; } return false ; }
is there an unaligned character at this position ?
