Re: [Seqan-dev] SA interval from indices

[Rahn, René <rene.maerker@fu-berlin.de>]

Hi Yue,

I am not sure, whether some one answered your question already?

Instead of using the finder interface you could directly use the VSTree Iterator.

Look at the docu here: http://docs.seqan.de/seqan/develop/specialization_VSTreeIterator.html#VSTreeIterator%23countOccurrences

It also has a little code example to show how to use the iterator to count occurrences.

IHTH, 

René

 

On 24 Jun 2015, at 00:07, Yue Gan <gany.fml@gmail.com> wrote:

Hi,

After created indices (I am using indexEsa), how do you search pattern by using them? 

I only know you can create a finder based on the indices, and search pattern using finder based on the tutorial. But finder sometimes does not seems very convenient to me. Sometime I only need the occ value of the pattern, not their position, so I have to do:

    int num_cout;

    while (find(Finder, "TATAA"))

    {

        ++num_cout;

    }

And I do not think this is the right way to do it.... Is there any other way that I can get the SAInterval directly?

Thanks!

Yue Gan

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René Rahn

Ph.D. Student

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Tel:  (+49) 30 838 75137

Mail: rene.rahn@fu-berlin.de

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Algorithmic Bioinformatics (ABI)

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