sorted_dictionary.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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 *      notice, this list of conditions and the following disclaimer.
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 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
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#pragma once

#include <nvbio/basic/types.h>
#include <nvbio/basic/iterator.h>

namespace nvbio {



struct SortedDictionaryNode
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    SortedDictionaryNode() {}

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    SortedDictionaryNode(const uint32 _begin, const uint32 _end, const uint32 _level) :
        begin( _begin ), end( _end ), level( _level ) {}

    uint32 begin;
    uint32 end;
    uint32 level;
};

template <uint32 ALPHABET_SIZE_T, typename Iterator>
struct SortedDictionarySuffixTrie
{
    const static uint32 ALPHABET_SIZE = ALPHABET_SIZE_T;

    typedef typename std::iterator_traits<Iterator>::value_type string_type;
    typedef SortedDictionaryNode                                node_type;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    SortedDictionarySuffixTrie(const Iterator seq, const uint32 size);

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    node_type root() const;

    template <typename Visitor>
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void children(const node_type node, Visitor& visitor) const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    bool is_leaf(const node_type node) const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 size(const node_type node) const;

private:
    Iterator m_seq;
    uint32   m_size;
};


} // namespace nvbio

#include <nvbio/trie/sorted_dictionary_inl.h>