seeds.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
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 * modification, are permitted provided that the following conditions are met:
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 *      names of its contributors may be used to endorse or promote products
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#pragma once

#include <nvbio/strings/string_set.h>
#include <nvbio/basic/numbers.h>
#include <nvbio/basic/vector.h>
#include <thrust/transform.h>
#include <thrust/scan.h>


namespace nvbio {



template <typename index_type, typename seed_functor, typename index_vector_type>
index_type enumerate_string_seeds(
    const index_type            string_len,
    const seed_functor          seeder,
          index_vector_type&    indices);

template <typename string_set_type, typename seed_functor, typename index_vector_type>
uint64 enumerate_string_set_seeds(
    const string_set_type       string_set,
    const seed_functor          seeder,
          index_vector_type&    indices);

template <typename index_type = uint32>
struct uniform_seeds_functor
{
    typedef index_type                                  argument_type;
    typedef index_type                                  result_type;
    typedef typename vector_type<index_type,2u>::type   range_type;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uniform_seeds_functor(const uint32 _len, const uint32 _interval) : len(_len), interval(_interval) {}

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    index_type operator() (const index_type length) const
    {
        uint32 n = 0;
        for (uint32 pos = 0; pos + len <= length; pos += interval)
            ++n;
        return n;
    }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    range_type seed(const uint32 length, const index_type i) const { return make_vector( i * interval, i * interval + len ); }

    const uint32 len;       
    const uint32 interval;  
};


} // namespace nvbio

#include <nvbio/strings/seeds_inl.h>