## SuffixTrees.jl

Julia implementation of the Ukkonen suffix tree algorithm
Author wherrera10
Popularity
2 Stars
Updated Last
9 Months Ago
Started In
September 2020

# SuffixTrees.jl

Julia implementation of the Ukkonen suffix tree algorithm

## Functions

``````mutable struct Node
children::Dict{Char,Int}
start::Int
ending::Int
suffixindex::Int
Node(strt = 0, endng = oo) = new(Dict{Char,Int}(), strt, endng, 0, -1)
end
``````

The suffix-tree's node and default constructor.

Note that these are referenced not by pointer but by an index into an array of nodes.

``````mutable struct SuffixTree
nodes::Vector{Node}
text::Vector{Char}
root::Int
position::Int
currentnode::Int
remainder::Int
activenode::Int
activelength::Int
activeedge::Int
end
``````

The SuffixTree struct.

``````function SuffixTree(str::String, addterminator = true, terminatorchar = Char(65129))
``````

SuffixTree constructor from string. Note that the string should have a terminator character at its end, usually '\$' or '#'. If addterminator is true (default) and the last character is not a unique terminator, will add one from a Unicode page (default is '﹩').

``````edgelength(st, n::Node)
``````

Return length of edge of a node (the portion of the sequence it covers) """

``````function newnode(st, start, ending)
``````

Make a node for the tree

``````function addsuffixlink(st, nodenum::Int)
``````

``````activeedge(st)
``````

Return active edge of tree

``````function walkdown!(st, currnode::Int)
``````

Walk down the tree to its active length

``````function extendsuffixtree(st, pos)
``````

Extend tree at pos

``````function setsuffixindexbyDFS(st, node, labelheight, verbose=false)
``````

Set the index of the leaves of the tree within the sequence

``````function dotraversal(st)
``````

Traverse the suffix tree

``````function getlongestrepeatedsubstring(st::SuffixTree, label="", printresult=true)
``````

Find the longest repeated suffix of the tree

## Example

``````using SuffixTrees

examples = [
("CAAAABAAAABD\\$", "AAAAB"),
("GEEKSFORGEEKS\\$", "GEEKS"),
("AAAAAAAAAA\\$", "AAAAAAAAA"),
("ABCDEFG\\$", ""),
("ABABABA\\$", "ABABA"),
("ATCGATCGA\\$", "ATCGA"),
("banana\\$", "ana"),
("abcpqrabpqpq\\$", "ab (or) pq"),
("pqrpqpqabab\\$", "ab (or) pq"),
("CAAAABDAAAABD\\$", "AAAABD"),
("CAAAABDAAAABD", "AAAABD"),  # this one gets an added terminator ﹩ by default
]

println("Test Longest Repeated Substring in:\n")
for (ex, ans) in examples
st = SuffixTree(ex)
println("Check: ", getlongestrepeatedsubstring(st), " == \$ans")
end
``````