Using the Sadakane Compressed Suffix Tree to Solve the All-Pairs Suffix-Prefix Problem

Algorithm 1

First method.

(1) 𝑖= The position in BP of the first child of the root (ignoring children which belong to the distinct separators)

(2) 𝑔←𝑟𝑎𝑛𝑘₍₎(𝑖)

(3) 𝑔←𝑔+1

(4) while   𝑖< The position in BP of the rightmostleaf in the tree do

(5)  𝑖←𝑠𝑒𝑙𝑒𝑐𝑡₍₎(𝑔)

(6)  if The node with the position 𝑖 in BP has a terminal edge then

(7)   Add the text position of 𝑖 to 𝐿_𝑣 where 𝑣 is the parent of the node which has a position 𝑖 in BP

(8) end if

(9)  𝑔←𝑔+1

(10) end while

(11) firstchild = The position of the first child of the root in BP

(12) for   𝑖= firstchild To rightmostleaf of the tree do

(13)  if isLeaf(𝑖) and (𝑖 is a Starting Position in a string 𝑓) then

(14)   for   𝑗= 1 to 𝑘  do

(15)    if   𝑗≠𝑓  then

(16)     Sol[𝑗,𝑓]=top(stack(𝑗))

(17)    end if

(18)   end for

(19)   Increment 𝑖 by 1 to avoid the closing parenthesis

(20)  else if   𝑖 is an opening parenthesis of an internal node 𝑣  then

(21)   for   𝑗=1 to size of 𝐿_𝑣  do

(22)    Push 𝐿_𝑣(𝑗) to the corresponding stack

(23)   end for

(24)  else if 𝑖 is a closing parenthesis of an internal node 𝑣  then

(25)   for   𝑗=1 to size of 𝐿_𝑣  do

(26)    Pop 𝐿_𝑣(𝑗) from the corresponding stack

(27)   end for

(28)  end if

(29) end for