Re: [Seqan-dev] IndexEsa and longest prefix search (single step of greedy LZW decomposition)
Hi Sebastian,
sounds like you want to do a simple prefix search of a pattern. That can be done with a top-down iterator, say iter, (that starts in the root node) which you move down along your not-indexed string with goDown(iter, "CCCGGGAAAT"); After that it stops in the node that still is a substring of the text, i.e. the longest prefix.
To get the occurrences or length of it use getOccurrences(iter) or repLength(iter)
Cheers,
David
--
David Weese weese@inf.fu-berlin.de
Freie Universität Berlin http://www.inf.fu-berlin.de/
Institut für Informatik Phone: +49 30 838 75137
Takustraße 9 Algorithmic Bioinformatics
14195 Berlin Room 020
Am 13.06.2013 um 10:00 schrieb Sebastian Wandelt <wandelt@informatik.hu-berlin.de>:
> Hi,
>
> I would like to use IndexEsa to find the longest infix which is a prefix of another (not indexed) string.
> This step is part of an algorithm to compute a greedy LZW-decomposition of a string with respect to a reference string.
>
> Example:
>
> Given an IndexEsa over AAAACCCCGGGGTTTT, I would like to have the longest prefix of CCCGGGAAAT, occurring as an infix in AAAACCCCGGGGTTTT.
> The result should be position 5 (and length 6), since the prefix CCCGGG can be found at position 5 (0-based string access) and is of length 6.
>
> Is there any ready code for solving this problem in Seqan? I think this should be a standard-operation for suffix trees.
> I haven't found any code that can be used directly, although I think that TopDown-Iterators might be the thing to go for.
>
> Thanks,
> Sebastian
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
