I'm working on modernizing Rosetta Code's infrastructure. Starting with communications. Please accept this time-limited open invite to RC's Slack.. --Michael Mol (talk) 20:59, 30 May 2020 (UTC)

Ukkonen’s suffix tree construction

From Rosetta Code
Task
Ukkonen’s suffix tree construction
You are encouraged to solve this task according to the task description, using any language you may know.

Suffix Trees are very useful in numerous string processing and computational biology problems.

The task is to create a function which implements Ukkonen’s algorithm to create a useful Suffix Tree as described:

Part 1
Part 2
Part 3
Part 4
Part 5
Part 6

Using Arithmetic-geometric mean/Calculate Pi generate the first 1000, 10000, and 100000 decimal places of pi. Using your implementation with an alphabet of 0 through 9 (plus $ say to make the tree explicit) find the longest repeated string in each list. Time your results and demonstrate that your implementation is linear (i.e. that 10000 takes approx. 10 times as long as 1000). You may vary the size of the lists of decimal places of pi to give reasonable answers.

Go[edit]

This is a translation of the C code here which is an extended form of the code in Part 6 of the task description for finding the longest repeated substring of a given string. In the interests of brevity, the extensive comments in the C version have been largely omitted. The C code doesn't compile as it stands but I have added a fix in the Talk Page.

For convenience I have included the code from the Arithmetic-geometric_mean/Calculate_Pi#Go task in the same package.

It takes around 25 seconds on my machine (Celeron @1.6GHz) to calculate the first 100,000 (or so) decimal places of Pi. Having done that, the timings for extracting the longest repeated sequence of digits are quick and fairly linear as expected.

As the task doesn't say whether overlapping sequences are to be counted, I've assumed that they are as this is what the algorithm naturally produces.

package main
 
import (
"fmt"
"math/big"
"time"
)
 
var maxChar = 128
 
type Node struct {
children []*Node
suffixLink *Node
start int
end *int
suffixIndex int
}
 
var (
text string
root *Node
lastNewNode *Node
activeNode *Node
activeEdge = -1
activeLength = 0
remainingSuffixCount = 0
leafEnd = -1
rootEnd *int
splitEnd *int
size = -1
)
 
func newNode(start int, end *int) *Node {
node := new(Node)
node.children = make([]*Node, maxChar)
node.suffixLink = root
node.start = start
node.end = end
node.suffixIndex = -1
return node
}
 
func edgeLength(n *Node) int {
if n == root {
return 0
}
return *(n.end) - n.start + 1
}
 
func walkDown(currNode *Node) bool {
if activeLength >= edgeLength(currNode) {
activeEdge += edgeLength(currNode)
activeLength -= edgeLength(currNode)
activeNode = currNode
return true
}
return false
}
 
func extendSuffixTree(pos int) {
leafEnd = pos
remainingSuffixCount++
lastNewNode = nil
for remainingSuffixCount > 0 {
if activeLength == 0 {
activeEdge = pos
}
if activeNode.children[text[activeEdge]] == nil {
activeNode.children[text[activeEdge]] = newNode(pos, &leafEnd)
if lastNewNode != nil {
lastNewNode.suffixLink = activeNode
lastNewNode = nil
}
} else {
next := activeNode.children[text[activeEdge]]
if walkDown(next) {
continue
}
if text[next.start+activeLength] == text[pos] {
if lastNewNode != nil && activeNode != root {
lastNewNode.suffixLink = activeNode
lastNewNode = nil
}
activeLength++
break
}
temp := next.start + activeLength - 1
splitEnd = &temp
split := newNode(next.start, splitEnd)
activeNode.children[text[activeEdge]] = split
split.children[text[pos]] = newNode(pos, &leafEnd)
next.start += activeLength
split.children[text[next.start]] = next
if lastNewNode != nil {
lastNewNode.suffixLink = split
}
lastNewNode = split
}
remainingSuffixCount--
if activeNode == root && activeLength > 0 {
activeLength--
activeEdge = pos - remainingSuffixCount + 1
} else if activeNode != root {
activeNode = activeNode.suffixLink
}
}
}
 
func setSuffixIndexByDFS(n *Node, labelHeight int) {
if n == nil {
return
}
if n.start != -1 {
// Uncomment line below to print suffix tree
// fmt.Print(text[n.start: *(n.end) +1])
}
leaf := 1
for i := 0; i < maxChar; i++ {
if n.children[i] != nil {
// Uncomment the 3 lines below to print suffix index
//if leaf == 1 && n.start != -1 {
// fmt.Printf(" [%d]\n", n.suffixIndex)
//}
leaf = 0
setSuffixIndexByDFS(n.children[i], labelHeight+edgeLength(n.children[i]))
}
}
if leaf == 1 {
n.suffixIndex = size - labelHeight
// Uncomment line below to print suffix index
//fmt.Printf(" [%d]\n", n.suffixIndex)
}
}
 
func buildSuffixTree() {
size = len(text)
temp := -1
rootEnd = &temp
root = newNode(-1, rootEnd)
activeNode = root
for i := 0; i < size; i++ {
extendSuffixTree(i)
}
labelHeight := 0
setSuffixIndexByDFS(root, labelHeight)
}
 
func doTraversal(n *Node, labelHeight int, maxHeight, substringStartIndex *int) {
if n == nil {
return
}
if n.suffixIndex == -1 {
for i := 0; i < maxChar; i++ {
if n.children[i] != nil {
doTraversal(n.children[i], labelHeight+edgeLength(n.children[i]),
maxHeight, substringStartIndex)
}
}
} else if n.suffixIndex > -1 && (*maxHeight < labelHeight-edgeLength(n)) {
*maxHeight = labelHeight - edgeLength(n)
*substringStartIndex = n.suffixIndex
}
}
 
func getLongestRepeatedSubstring(s string) {
maxHeight := 0
substringStartIndex := 0
doTraversal(root, 0, &maxHeight, &substringStartIndex)
// Uncomment line below to print maxHeight and substringStartIndex
// fmt.Printf("maxHeight %d, substringStartIndex %d\n", maxHeight, substringStartIndex)
if s == "" {
fmt.Printf("  %s is: ", text)
} else {
fmt.Printf("  %s is: ", s)
}
k := 0
for ; k < maxHeight; k++ {
fmt.Printf("%c", text[k+substringStartIndex])
}
if k == 0 {
fmt.Print("No repeated substring")
}
fmt.Println()
}
 
func calculatePi() *big.Float {
one := big.NewFloat(1)
two := big.NewFloat(2)
four := big.NewFloat(4)
prec := uint(325 * 1024) // enough to calculate Pi to 100,182 decimal digits
 
a := big.NewFloat(1).SetPrec(prec)
g := new(big.Float).SetPrec(prec)
 
// temporary variables
t := new(big.Float).SetPrec(prec)
u := new(big.Float).SetPrec(prec)
 
g.Quo(a, t.Sqrt(two))
sum := new(big.Float)
pow := big.NewFloat(2)
 
for a.Cmp(g) != 0 {
t.Add(a, g)
t.Quo(t, two)
g.Sqrt(u.Mul(a, g))
a.Set(t)
pow.Mul(pow, two)
t.Sub(t.Mul(a, a), u.Mul(g, g))
sum.Add(sum, t.Mul(t, pow))
}
 
t.Mul(a, a)
t.Mul(t, four)
pi := t.Quo(t, u.Sub(one, sum))
return pi
}
 
func main() {
tests := []string{
"GEEKSFORGEEKS$",
"AAAAAAAAAA$",
"ABCDEFG$",
"ABABABA$",
"ATCGATCGA$",
"banana$",
"abcpqrabpqpq$",
"pqrpqpqabab$",
}
fmt.Println("Longest Repeated Substring in:\n")
for _, test := range tests {
text = test
buildSuffixTree()
getLongestRepeatedSubstring("")
}
fmt.Println()
 
pi := calculatePi()
piStr := fmt.Sprintf("%v", pi)
piStr = piStr[2:] // remove initial 3.
numbers := []int{1e3, 1e4, 1e5}
maxChar = 58
for _, number := range numbers {
start := time.Now()
text = piStr[0:number] + "$"
buildSuffixTree()
getLongestRepeatedSubstring(fmt.Sprintf("first %d d.p. of Pi", number))
elapsed := time.Now().Sub(start)
fmt.Printf(" (this took %s)\n\n", elapsed)
}
}
Output:

Sample run:

Longest Repeated Substring in:

  GEEKSFORGEEKS$ is: GEEKS
  AAAAAAAAAA$ is: AAAAAAAAA
  ABCDEFG$ is: No repeated substring
  ABABABA$ is: ABABA
  ATCGATCGA$ is: ATCGA
  banana$ is: ana
  abcpqrabpqpq$ is: ab
  pqrpqpqabab$ is: ab

  first 1000 d.p. of Pi is: 23846
  (this took 7.728858ms)

  first 10000 d.p. of Pi is: 7111369
  (this took 57.524478ms)

  first 100000 d.p. of Pi is: 041021944
  (this took 599.770281ms)

Julia[edit]

Translation of: Go

Uses array indices instead of the Go version's node pointers.

const oo = typemax(Int)
 
"""The suffix-tree's node."""
mutable struct Node
children::Dict{Char, Int}
start::Int
ending::Int
suffixlink::Int
suffixindex::Int
end
 
Node() = Node(Dict(), 0, oo, 0, -1)
Node(start, ending) = Node(Dict(), start, ending, 0, -1)
 
""" Ukkonen Suffix-Tree """
mutable struct SuffixTree
nodes::Vector{Node}
text::Vector{Char}
root::Int
position::Int
currentnode::Int
needsuffixlink::Int
remainder::Int
activenode::Int
activelength::Int
activeedge::Int
end
 
edgelength(st, n::Node) = min(n.ending, st.position + 1) - n.start
 
function newnode(st, start, ending)
st.currentnode += 1
st.nodes[st.currentnode] = Node(start, ending)
return st.currentnode
end
 
function SuffixTree(str::String)
nodes = [Node() for _ in 1:length(str) * 2]
st = SuffixTree(nodes, [c for c in str], 1, 0, 0, 0, 0, 1, 1, 1)
st.root = newnode(st, 0, 0)
st.activenode = st.root
for i in 1:length(st.text)
extendsuffixtree(st, i)
end
setsuffixindexbyDFS(st, st.nodes[st.root], 0)
return st
end
 
function addsuffixlink(st, nodenum::Int)
if st.needsuffixlink > 0
st.nodes[st.needsuffixlink].suffixlink = nodenum
end
st.needsuffixlink = nodenum
end
 
activeedge(st) = st.text[st.activeedge]
 
function walkdown!(st, currnode::Int)
len = edgelength(st, st.nodes[currnode])
st.activelength < len && return false
st.activeedge += len
st.activelength -= len
st.activenode = currnode
return true
end
 
function extendsuffixtree(st, pos)
st.position = pos
st.needsuffixlink = 0
st.remainder += 1
while st.remainder > 0
st.activelength == 0 && (st.activeedge = st.position)
if !haskey(st.nodes[st.activenode].children, activeedge(st))
nodenum = newnode(st, st.position, oo)
st.nodes[st.activenode].children[activeedge(st)] = nodenum
addsuffixlink(st, st.activenode)
else
next = st.nodes[st.activenode].children[activeedge(st)]
walkdown!(st, next) && continue
if st.text[st.nodes[next].start + st.activelength] == st.text[pos]
addsuffixlink(st, st.activenode)
st.activelength += 1
break
end
splt = newnode(st, st.nodes[next].start, st.nodes[next].start + st.activelength)
st.nodes[st.activenode].children[activeedge(st)] = splt
nodenum = newnode(st, st.position, oo)
st.nodes[splt].children[st.text[pos]] = nodenum
st.nodes[next].start += st.activelength
st.nodes[splt].children[st.text[st.nodes[next].start]] = next
addsuffixlink(st, splt)
end
st.remainder -= 1
if st.activenode == st.root && st.activelength > 0
st.activelength -= 1
st.activeedge = st.position - st.remainder + 1
elseif st.activenode != st.root
st.activenode = st.nodes[st.activenode].suffixlink
end
end
end
 
function setsuffixindexbyDFS(st, node, labelheight, verbose=false)
verbose && node.start > 0 && print(st.text[node.start:min(node.ending, length(st.text))])
isleaf = true
for child in map(v -> st.nodes[v], collect(values(node.children)))
verbose && isleaf && node.start > 0 && println(" [", node.suffixindex, "]")
isleaf = false
setsuffixindexbyDFS(st, child, labelheight + edgelength(st, child))
end
if isleaf
idx = length(st.text) - labelheight
node.suffixindex = idx
verbose && println(" [$idx]")
end
end
 
function dotraversal(st)
maxheight, substringstartindices = 0, [0]
function traversal(node::Node, labelheight)
if node.suffixindex == -1
for child in map(v -> st.nodes[v], collect(values(node.children)))
traversal(child, labelheight + edgelength(st, child))
end
elseif maxheight < labelheight - edgelength(st, node)
maxheight = labelheight - edgelength(st, node)
substringstartindices = [node.suffixindex + 1]
elseif maxheight == labelheight - edgelength(st, node)
push!(substringstartindices, node.suffixindex + 1)
end
end
traversal(st.nodes[st.root], 0)
return maxheight, substringstartindices
end
 
function getlongestrepeatedsubstring(st::SuffixTree, label="", printresult=true)
len, starts = dotraversal(st)
substring = len == 0 ? "" :
join(unique(map(x -> String(st.text[x:x+len-1]), starts)), " (or) ")
if printresult
print(" ", label == "" ? String(st.text) : label, ": ")
println(len == 0 ? "No repeated substring." : substring)
end
return substring
end
 
function testsuffixtree()
tests = [
"CAAAABAAAABD\$",
"GEEKSFORGEEKS\$",
"AAAAAAAAAA\$",
"ABCDEFG\$",
"ABABABA\$",
"ATCGATCGA\$",
"banana\$",
"abcpqrabpqpq\$",
"pqrpqpqabab\$",
]
println("Longest Repeated Substring in:\n")
for test in tests
st = SuffixTree(test)
getlongestrepeatedsubstring(st)
end
println()
sπ = ""
setprecision(4000000) do
sπ = string(BigFloat(π))[3:end]
end
for number in [1000, 10000, 100000, 1000000]
text = sπ[1:number] * "\$"
@time begin
st = SuffixTree(text)
getlongestrepeatedsubstring(st, "first $number d.p. of π")
end
end
end
 
testsuffixtree()
 
Output:
Longest Repeated Substring in:

  CAAAABAAAABD: AAAAB
  GEEKSFORGEEKS: GEEKS
  AAAAAAAAAA: AAAAAAAAA
  ABCDEFG: No repeated substring.
  ABABABA: ABABA
  ATCGATCGA: ATCGA
  banana: ana
  abcpqrabpqpq: ab (or) pq
  pqrpqpqabab: ab (or) pq

  first 1000 d.p. of π: 60943 (or) 42019 (or) 82534 (or) 99999 (or) 93751 (or) 23846 (or) 33446
  0.003336 seconds (34.86 k allocations: 4.252 MiB)
  first 10000 d.p. of π: 7111369 (or) 8530614
  0.038749 seconds (351.60 k allocations: 42.460 MiB, 16.54% gc time)
  first 100000 d.p. of π: 134926158 (or) 041021944 (or) 201890888
  0.533892 seconds (3.52 M allocations: 425.035 MiB, 22.42% gc time)
  first 1000000 d.p. of π: 756130190263
  6.008879 seconds (35.25 M allocations: 4.152 GiB, 23.20% gc time)

Phix[edit]

Translation of: Go
-- demo/rosetta/Ukkonens_Suffix_Tree.exw
with javascript_semantics
integer maxChar = 'z'
 
sequence children = {},
         suffixLinks = {},
         starts = {},
         endIndices = {},
         suffixIndices = {},
         leaves = {}

function new_leaf(integer v=0)
    leaves = append(leaves,v)
    return length(leaves)
end function

string text
integer splitEndIdx,
        rootEndIdx,
        leafEndIdx = new_leaf(),
        root = NULL,
        lastNewNode,
        activeNode,
        activeEdge = -1,
        activeLength = 0,
        remainingSuffixCount = 0,
        size = -1
 
function newNode(integer start, finishIdx, bool bKids=false)
    children = append(children,iff(bKids?repeat(NULL,maxChar):0))
    suffixLinks = append(suffixLinks,root)
    starts = append(starts,start)
    endIndices = append(endIndices,finishIdx)
    suffixIndices = append(suffixIndices,-1)
    return length(children)
end function
 
function edgeLength(integer n)
    return iff(n==root?0:leaves[endIndices[n]] - starts[n] + 1)
end function
 
function walkDown(integer currNode)
    integer l = edgeLength(currNode)
    if activeLength >= l then
        activeEdge += l
        activeLength -= l
        activeNode = currNode
        return true
    end if
    return false
end function
 
procedure extendSuffixTree(integer pos)
    leaves[leafEndIdx] = pos
    remainingSuffixCount += 1
    lastNewNode = NULL
    while remainingSuffixCount > 0 do
        if activeLength == 0 then
            activeEdge = pos
        end if
        integer ta = text[activeEdge]
        bool ca0 = children[activeNode]=0
        integer next = iff(ca0?NULL:children[activeNode][ta])
        if next==null then
            if ca0 then
                children[activeNode] = repeat(NULL,maxChar)
            end if
            children[activeNode][ta] = newNode(pos, leafEndIdx)
            if lastNewNode!=NULL then
                suffixLinks[lastNewNode] = activeNode
                lastNewNode = NULL
            end if
        else
            if walkDown(next) then
                continue
            end if
            integer tp = text[pos]
            if text[starts[next]+activeLength] == tp then
                if lastNewNode!=NULL and activeNode!=root then
                    suffixLinks[lastNewNode] = activeNode
                    lastNewNode = NULL
                end if
                activeLength += 1
                exit
            end if
            integer temp = starts[next] + activeLength - 1
            splitEndIdx = new_leaf(temp)
            integer splitnode = newNode(starts[next], splitEndIdx, true)
            ta = text[activeEdge]
            children[activeNode][ta] = splitnode
            children[splitnode][tp] = newNode(pos, leafEndIdx)
            starts[next] += activeLength
            children[splitnode][text[starts[next]]] = next
            if lastNewNode!=NULL then
                suffixLinks[lastNewNode] = splitnode
            end if
            lastNewNode = splitnode
        end if
        remainingSuffixCount -= 1
        if activeNode==root and activeLength>0 then
            activeLength -= 1
            activeEdge = pos - remainingSuffixCount + 1
        elsif activeNode!=root then
            activeNode = suffixLinks[activeNode]
        end if
    end while
end procedure
 
procedure setSuffixIndexByDFS(integer n, labelHeight)
    if n!=NULL then
        if children[n]=0 then
            suffixIndices[n] = size - labelHeight
        else
            bool leaf = true
            for i=1 to maxChar do
                integer nci = children[n][i]
                if nci!=NULL then
                    leaf = false
                    setSuffixIndexByDFS(nci, labelHeight+edgeLength(nci))
                end if
            end for
            if leaf then ?9/0 end if -- (sanity check)
        end if
    end if
end procedure
 
procedure buildSuffixTree()
    size = length(text)
    rootEndIdx = new_leaf(-1)
    root = newNode(-1, rootEndIdx)
    activeNode = root
    for i=1 to size do
        extendSuffixTree(i)
    end for
    integer labelHeight = 0
    setSuffixIndexByDFS(root, labelHeight)
end procedure
 
procedure doTraversal(integer n, labelHeight, maxHeightIdx, substringStartIndex)
    if n!=NULL then
        integer nsi = suffixIndices[n], newHeight
        if nsi == -1 then
            for i=1 to maxChar do
                integer nci = children[n][i]
                if nci!=NULL then
                    newHeight = labelHeight+edgeLength(nci)
                    doTraversal(nci, newHeight, maxHeightIdx, substringStartIndex)
                end if
            end for
        elsif nsi > -1 then
            newHeight = labelHeight-edgeLength(n)
            if leaves[maxHeightIdx]<newHeight then
                leaves[maxHeightIdx] = newHeight
                leaves[substringStartIndex] = nsi
            end if
        end if
    end if
end procedure
 
function getLongestRepeatedSubstring()
    integer maxHeightIdx = new_leaf(),
            substringStartIndex = new_leaf()
    doTraversal(root, 0, maxHeightIdx, substringStartIndex)
    integer maxHeight = leaves[maxHeightIdx],
            start = leaves[substringStartIndex]
    string t = iff(maxHeight=0?"No repeated substring"
                              :text[start+1..start+maxHeight])
    return t
end function
 
constant tests = {"CAAAABAAAABD$",
                  "GEEKSFORGEEKS$",
                  "AAAAAAAAAA$",
                  "ABCDEFG$",
                  "ABABABA$",
                  "ATCGATCGA$",
                  "banana$",
                  "abcpqrabpqpq$",
                  "pqrpqpqabab$"}
printf(1,"Longest Repeated Substring in:\n")
for i=1 to length(tests) do
    text = tests[i]
    buildSuffixTree()
    printf(1,"  %s is: %s\n", {text,getLongestRepeatedSubstring()})
end for
printf(1,"\n")
 
include mpfr.e
string piStr
if platform()=JS then
    mpfr pi = mpfr_init(0,-1001) -- (set precision to 1,000 dp, plus the "3.")
    mpfr_const_pi(pi)
    piStr = mpfr_get_fixed(pi,1000) -- (all we can really manage under pwa/p2js)
else
    -- gmp crashes when I try 100,000 dp, so just get from file
    piStr = get_text(`E:\downloads\misc\arm\pi-10million.txt`)
end if
piStr = piStr[3..$] -- discard leading "3."
maxChar = '9'
for i=3 to iff(platform()=JS?3:6) do
    atom t0 = time()
    integer n = power(10,i)
    text = piStr[1..n] & "$"
    buildSuffixTree()
    string r = getLongestRepeatedSubstring(),
           e = elapsed(time()-t0)
    printf(1,"  first %,d d.p. of Pi is: %s (%s)\n", {n,r,e})
end for
Output:
Longest Repeated Substring in:
  CAAAABAAAABD$ is: AAAAB
  GEEKSFORGEEKS$ is: GEEKS
  AAAAAAAAAA$ is: AAAAAAAAA
  ABCDEFG$ is: No repeated substring
  ABABABA$ is: ABABA
  ATCGATCGA$ is: ATCGA
  banana$ is: ana
  abcpqrabpqpq$ is: ab
  pqrpqpqabab$ is: ab

  first 1,000 d.p. of Pi is: 23846 (0s)
  first 10,000 d.p. of Pi is: 7111369 (0.0s)
  first 100,000 d.p. of Pi is: 041021944 (0.3s)
  first 1,000,000 d.p. of Pi is: 756130190263 (3.2s)

Note that mpfr_const_pi() struggles to generate more than 1,000 digits of pi under pwa/p2js [and will continue to do so unless someone graciously donates a decent/fast Chudnovsky method in pure Phix or JavaScript...]

Wren[edit]

Translation of: Go
Library: Wren-big
Library: Wren-dynamic
Library: Wren-trait

As it would take a very long time to calculate the first 100,000 digits of Pi using the code from the Arithmetic-geometric_mean/Calculate_Pi#Wren task, I have instead saved the digits produced by the Go entry to a file (which only takes a few seconds) and then loaded that into the Wren script.

Having done that, the timings for extracting the longest repeated sequence of digits are reasonably quick and fairly linear as expected.

import "/big" for BigRat
import "/dynamic" for Struct
import "/trait" for ByRef
import "io" for File
 
var maxChar = 128
 
var Node = Struct.create("Node", ["children", "suffixLink", "start", "pEnd", "suffixIndex"])
 
var text = ""
var root = null
var lastNewNode = null
var activeNode = null
var activeEdge = -1
var activeLength = 0
var remainingSuffixCount = 0
var pLeafEnd = ByRef.new(-1)
var pRootEnd = null
var pSplitEnd = null
var size = -1
 
var newNode = Fn.new { |start, pEnd|
var children = List.filled(maxChar, null)
var suffixLink = root
var suffixIndex = -1
return Node.new(children, suffixLink, start, pEnd, suffixIndex)
}
 
var edgeLength = Fn.new { |n|
if (n == root) return 0
return n.pEnd.value - n.start + 1
}
 
var walkDown = Fn.new { |currNode|
var el = edgeLength.call(currNode)
if (activeLength >= el) {
activeEdge = activeEdge + el
activeLength = activeLength - el
activeNode = currNode
return true
}
return false
}
 
var extendSuffixTree = Fn.new { |pos|
pLeafEnd.value = pos
remainingSuffixCount = remainingSuffixCount + 1
lastNewNode = null
while (remainingSuffixCount > 0) {
if (activeLength == 0) activeEdge = pos
if (!activeNode.children[text[activeEdge].bytes[0]]) {
activeNode.children[text[activeEdge].bytes[0]] = newNode.call(pos, pLeafEnd)
if (lastNewNode) {
lastNewNode.suffixLink = activeNode
lastNewNode = null
}
} else {
var next = activeNode.children[text[activeEdge].bytes[0]]
if (walkDown.call(next)) continue
if (text[next.start + activeLength] == text[pos]) {
if (lastNewNode && activeNode != root) {
lastNewNode.suffixLink = activeNode
lastNewNode = null
}
activeLength = activeLength + 1
break
}
var temp = next.start + activeLength - 1
pSplitEnd = ByRef.new(temp)
var split = newNode.call(next.start, pSplitEnd)
activeNode.children[text[activeEdge].bytes[0]] = split
split.children[text[pos].bytes[0]] = newNode.call(pos, pLeafEnd)
next.start = next.start + activeLength
split.children[text[next.start].bytes[0]] = next
if (lastNewNode) lastNewNode.suffixLink = split
lastNewNode = split
}
remainingSuffixCount = remainingSuffixCount - 1
if (activeNode == root && activeLength > 0) {
activeLength = activeLength - 1
activeEdge = pos - remainingSuffixCount + 1
} else if (activeNode != root) {
activeNode = activeNode.suffixLink
}
}
}
 
var setSuffixIndexByDFS // recursive
setSuffixIndexByDFS = Fn.new { |n, labelHeight|
if (!n) return
if (n.start != -1) {
// Uncomment line below to print suffix tree
// System.write(text[n.start..n.pEnd.value])
}
var leaf = 1
for (i in 0...maxChar) {
if (n.children[i]) {
// Uncomment the 3 lines below to print suffix index
// if (leaf == 1 && n.start != -1) {
// System.print(" [%(n.suffixIndex)]")
// }
leaf = 0
setSuffixIndexByDFS.call(n.children[i], labelHeight + edgeLength.call(n.children[i]))
}
}
if (leaf == 1) {
n.suffixIndex = size - labelHeight
// Uncomment line below to print suffix index
// System.print(" [%(n.suffixIndex)]")
}
}
 
var buildSuffixTree = Fn.new {
size = text.count
var temp = -1
pRootEnd = ByRef.new(temp)
root = newNode.call(-1, pRootEnd)
activeNode = root
for (i in 0...size) extendSuffixTree.call(i)
var labelHeight = 0
setSuffixIndexByDFS.call(root, labelHeight)
}
 
var doTraversal // recursive
doTraversal = Fn.new { |n, labelHeight, pMaxHeight, pSubstringStartIndex|
if (!n) return
if (n.suffixIndex == -1) {
for (i in 0...maxChar) {
if (n.children[i]) {
doTraversal.call(n.children[i], labelHeight + edgeLength.call(n.children[i]),
pMaxHeight, pSubstringStartIndex)
}
}
} else if (n.suffixIndex > -1 && (pMaxHeight.value < labelHeight - edgeLength.call(n))) {
pMaxHeight.value = labelHeight - edgeLength.call(n)
pSubstringStartIndex.value = n.suffixIndex
}
}
 
var getLongestRepeatedSubstring = Fn.new { |s|
var maxHeight = 0
var substringStartIndex = 0
var pMaxHeight = ByRef.new(maxHeight)
var pSubstringStartIndex = ByRef.new(substringStartIndex)
doTraversal.call(root, 0, pMaxHeight, pSubstringStartIndex)
maxHeight = pMaxHeight.value
substringStartIndex = pSubstringStartIndex.value
// Uncomment line below to print maxHeight and substringStartIndex
// System.print("maxHeight %(maxHeight), substringStartIndex %(substringStartIndex)")
if (s == "") {
System.write("  %(text) is: ")
} else {
System.write("  %(s) is: ")
}
var k = 0
while (k < maxHeight) {
System.write(text[k + substringStartIndex])
k = k + 1
}
if (k == 0) {
System.write("No repeated substring")
}
System.print()
}
 
var tests = [
"GEEKSFORGEEKS$",
"AAAAAAAAAA$",
"ABCDEFG$",
"ABABABA$",
"ATCGATCGA$",
"banana$",
"abcpqrabpqpq$",
"pqrpqpqabab$",
]
System.print("Longest Repeated Substring in:\n")
for (test in tests) {
text = test
buildSuffixTree.call()
getLongestRepeatedSubstring.call("")
}
System.print()
 
// load pi to 100,182 digits
var piStr = File.read("pi_100000.txt")
piStr = piStr[2..-1] // remove initial 3.
var numbers = [1e3, 1e4, 1e5]
maxChar = 58
for (number in numbers) {
var start = System.clock
text = piStr[0...number] + "$"
buildSuffixTree.call()
getLongestRepeatedSubstring.call("first %(number) d.p. of Pi")
var elapsed = (System.clock - start) * 1000
System.print(" (this took %(elapsed) ms)\n")
}
Output:
Longest Repeated Substring in:

  GEEKSFORGEEKS$ is: GEEKS
  AAAAAAAAAA$ is: AAAAAAAAA
  ABCDEFG$ is: No repeated substring
  ABABABA$ is: ABABA
  ATCGATCGA$ is: ATCGA
  banana$ is: ana
  abcpqrabpqpq$ is: ab
  pqrpqpqabab$ is: ab

  first 1000 d.p. of Pi is: 23846
  (this took 9.987 ms)

  first 10000 d.p. of Pi is: 7111369
  (this took 89.12 ms)

  first 100000 d.p. of Pi is: 041021944
  (this took 1031.072 ms)