suffix_trie.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
 *    * Neither the name of the NVIDIA CORPORATION nor the
 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

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

namespace nvbio {




enum TrieType { CompressedTrie, UncompressedTrie };

template <uint32 ALPHABET_SIZE_T, TrieType TYPE_T>
struct TrieNode
{
    const static uint32 ALPHABET_SIZE = ALPHABET_SIZE_T;

    static const uint32     invalid_node = uint32(-1);
    static const TrieType   trie_type    = TYPE_T;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    TrieNode();

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    TrieNode(const uint32 _child, const uint32 _mask);

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    bool is_leaf() const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 child() const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 child(const uint32 c) const;
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 nth_child(const uint32 c) const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 first_child() const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 mask() const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void set_child_bit(const uint32 c);

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 child_bit(const uint32 c) const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void set_size(const uint32 size);

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 size() const;

    uint32 m_child;
    uint32 m_mask;
    uint32 m_size;
};

template <TrieType TYPE_T>
struct TrieNode5
{
    const static uint32 ALPHABET_SIZE = 5;

    static const uint32     invalid_node = uint32(-1);
    static const TrieType   trie_type    = TYPE_T;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    TrieNode();

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    TrieNode(const uint32 _child, const uint32 _mask);

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    bool is_leaf() const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 child() const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 child(const uint32 c) const;
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 nth_child(const uint32 c) const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 first_child() const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 mask() const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void set_child_bit(const uint32 c);

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 child_bit(const uint32 c) const;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void set_size(const uint32 size);

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    uint32 size() const;

    uint32 m_child;
    uint32 m_mask:5, m_size:27;
};

template <TrieType TYPE_T>
struct TrieNode<2,TYPE_T> : public TrieNode5
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    TrieNode(const uint32 _child, const uint32 _mask) : TrieNode5( _child, _mask ) {}
};
template <TrieType TYPE_T>
struct TrieNode<3,TYPE_T> : public TrieNode5
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    TrieNode(const uint32 _child, const uint32 _mask) : TrieNode5( _child, _mask ) {}
};
template <TrieType TYPE_T>
struct TrieNode<4,TYPE_T> : public TrieNode5
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    TrieNode(const uint32 _child, const uint32 _mask) : TrieNode5( _child, _mask ) {}
};
template <TrieType TYPE_T>
struct TrieNode<5,TYPE_T> : public TrieNode5
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    TrieNode(const uint32 _child, const uint32 _mask) : TrieNode5( _child, _mask ) {}
};


template <uint32 ALPHABET_SIZE_T, typename NodeIterator>
struct SuffixTrie
{
    const static uint32 ALPHABET_SIZE = ALPHABET_SIZE_T;

    typedef typename std::iterator_traits<NodeIterator>::value_type node_type;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    SuffixTrie() {}

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    SuffixTrie(const NodeIterator seq);

    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;

    const NodeIterator& nodes() const { return m_seq; }

private:
    NodeIterator m_seq;
};


template <typename TrieType, typename NodeVector>
void build_suffix_trie(
    const TrieType&     in_trie,
    NodeVector&         out_nodes);


} // namespace nvbio

#include <nvbio/trie/suffix_trie_inl.h>