KGST

Library

A library containing the implementation of a K-Truncated Generalized Suffix Tree using Ukkonen's Algorithm, along with a CLI tool to quickly build and serialize KGST's.

Usage

CLI tool to build and serialize K-Truncated Generalized Suffix trees

Usage: gst [COMMAND]

Commands: build Build suffix tree index from reference fasta file help Print this message or the help of the given subcommand(s)

Options: -h, --help Print help -V, --version Print version

lib.rs:

K-Truncated Generalized Suffix Tree

Implementation of the truncated suffix tree construction of which is performed in linear time

Examples

use generalized_suffix_tree::suffix_tree::KGST;

// Initalize empty tree
let mut tree: KGST<char, String> = KGST::new('$');

// insert item with corresponding item id
let item_string:Vec<char> = "MKAILVVLLYTFTTADADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLENRHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTAGSWSYIVETSNPDNGTCYPGDFINYEELREQLSSVSSFEKFEIFPKTSSWPNHDTNRGVTAACPHDGAKSFYRNLLWLVKKEKENSYPMINKSYTNNKGKEVLVLWAIHHPATSADQQSLYQNANAYVFVGSSKYSKKFEPEIAARPKVRDQAGRMKYYWTLVEPGDKITFEATGNLVVPIYAFALKRNSGSGIIISDTSVHDCDTTCQTPNGAINTSLPFQNIHPVTIGECPKYVKSTKLRMATGLRNIPSIQSRGLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADLKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNHLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDDTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI".chars().collect();
let item_id:String = "World".to_string();
tree.insert(item_id.clone(), item_string.clone(),&0);


// Query if some string is a substring in the tree
let substring_match = tree.substring_match(&item_string[i..i+max_depth+1]);

// Query if some string is a suffix in the tree
let suffix_match = tree.suffix_match(&item_string[i..i+max_depth+1]);

// Clear tree
tree.clear();