suffix-tree

I'm searching for suffix tree library (that has linear time construction), and all I found is PATL, but PATL has no documentation and I can't figure out any of the examples. So is there a suffix tree library for c++ that has a decent documentation? PATL home : http://code.google.com/p/patl/ EDIT: Motivation: I need to process large amount of strings and find the frequent common substrings, and report if more than n occurrences of any substring occurred within t seconds. I implemented a tree (with counter in the nodes, actually it isn't a counter but an std::vector of visit times since like I

I'm implementing Ukkonen's algorithm, which requires that all leaves of a tree contain a reference to the same integer, and I'm doing it in Haskell to learn more about the language. However, I'm having a hard time writing out a data type that does this. -- Node has children, indexes of info on the edge -- to it, and an optional suffix link. -- Leaf has a beginning index of the info, but the -- end index is always an incrementing variable index. data STree = Node [STree] (Int, Int) (Maybe STree) | Leaf (Int, ??? ) How can I put the reference in the Leaf type declaration? 来源： https:/

I need to find the longest non-overlapping repeated substring in a String. I have the suffix tree and suffix array of the string available. When overlapping is allowed, the answer is trivial (deepest parent node in suffix tree). For example for String = "acaca" If overlapping is allowed, the answer is "aca" but when overlapping is not allowed, the answer is "ac" or "ca". I need the algorithm or high level idea only. P.S.: I tried but there is no clear answer I can find on web. Generate suffix array and sort in O(nlogn).ps: There is more effective algorithm like DC3 and Ukkonen algorithm.

I'm looking for a short, simple suffix tree building/usage algorithm in Java. The best I've found so far lies withing the Semantic Discovery Toolkit, but the implementation is several thousand lines long and spans several classes. Ideally, the implementation would be as short as possible and span no more than a few hundred lines. Does anyone have such an implementation? I just finished a Java implementation of a suffix tree. In my blog entry you can find out more about suffix trees, see how to use my library, as well as download and build the library using Subversion and Maven. Yes, it's

I am trying to pass BioPython sequences to Ilya Stepanov's implementation of Ukkonen's suffix tree algorithm in iPython's notebook environment. I am stumbling on the argparse component. I have never had to deal directly with argparse before. How can I use this without rewriting main()? By the by, this writeup of Ukkonen's algorithm is fantastic . I've had a similar problem before, but using optparse instead of argparse . You don't need to change anything in the original script, just assign a new list to sys.argv like so: if __name__ == "__main__": from Bio import SeqIO path = '/path/to

I came across below program which looks perfect. Per me its time complexity is nlogn where n is the length of String. n for storing different strings,nlog for sorting, n for comparison. So time complexity is nlogn. Space complexity is n for storing the storing n substrings My question is can it be further optimized ? public class LRS { // return the longest common prefix of s and t public static String lcp(String s, String t) { int n = Math.min(s.length(), t.length()); for (int i = 0; i < n; i++) { if (s.charAt(i) != t.charAt(i)) return s.substring(0, i); } return s.substring(0, n); } //