question: 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 ; }
target:  is there an unaligned character at this position?