A Practical and Scalable Tool to Find Overlaps between Sequences

Algorithm 3

Finding all-pairs suffix-prefix.

(1) Function findallpairs(node ptr)

(2) for each string in Group   do

(3)   is the first character in

(4)  while   is not an ending character in   do

(5)    = position of

(6)    = ptr; ; ;

(7)   while true do

(8)    if the character in position is the ending character in   then

(9)     for each string in .range do

(10)       if the suffix prefix match between and   then

(11)        is a suffix prefix match ( and )

(12)       end if

(13)      end for

(14)      break; 

(15)    end if

(16)    if  .  then

(17)       = character in position in

(18)       = the character to which is pointing

(19)      if   =   then

(20)       ++; ++; ++;

(21)      else

(22)       break

(23)     end if

(24)    else

(25)       = character in position in

(26)      if there is a branch for the , labeled by   then

(27)        = .branch()

(28)       ++; ++; ++;

(29)     else

(30)       break

(31)      end if

(32)    end if 

(33)   end while

(34)    is the next character in

(35)  end while

(36) end for