Re: [Seqan-dev] IndexEsa and longest prefix search (single step of greedy LZW decomposition)

["Weese, David" <weese@campus.fu-berlin.de>]

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/
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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
> 
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