https://github.com/wherrera10/suffixtrees.jl

Julia implementation of the Ukkonen suffix tree algorithm
https://github.com/wherrera10/suffixtrees.jl

julia-package suffix-tree

Last synced: about 1 month ago
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Julia implementation of the Ukkonen suffix tree algorithm

• Host: GitHub
• URL: https://github.com/wherrera10/suffixtrees.jl
• Owner: wherrera10
• License: bsd-2-clause
• Created: 2020-09-27T08:10:24.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2023-02-20T19:59:21.000Z (almost 2 years ago)
• Last Synced: 2024-11-11T08:46:36.570Z (about 2 months ago)
• Topics: julia-package, suffix-tree
• Language: Julia
• Homepage:
• Size: 114 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# SuffixTrees.jl

Julia implementation of the Ukkonen suffix tree algorithm



## Functions

    mutable struct Node

        children::Dict{Char,Int}

        start::Int

        ending::Int

        suffixlink::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

	    needsuffixlink::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)

    

Add a link to tree





    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