filter.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
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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/qgram/qgram.h>
#include <nvbio/basic/types.h>
#include <nvbio/basic/numbers.h>
#include <nvbio/basic/vector.h>
#include <nvbio/basic/algorithms.h>
#include <nvbio/basic/exceptions.h>
#include <nvbio/basic/cuda/sort.h>
#include <nvbio/basic/cuda/primitives.h>
#include <thrust/sort.h>
#include <thrust/scan.h>
#include <thrust/iterator/constant_iterator.h>
#include <thrust/iterator/counting_iterator.h>

namespace nvbio {


template <typename system_tag, typename qgram_index_type, typename query_iterator, typename index_iterator>
struct QGramFilter {};


template <typename qgram_index_type, typename query_iterator, typename index_iterator>
struct QGramFilter<host_tag, qgram_index_type, query_iterator, index_iterator>
{
    typedef host_tag            system_tag;

    typedef typename plain_view_subtype<const qgram_index_type>::type qgram_index_view;

    typedef typename qgram_index_type::coord_type coord_type;   

    typedef typename if_equal<coord_type, uint32, uint2,  uint4>::type  hit_type;
    typedef typename if_equal<coord_type, uint32, uint32, uint2>::type  diagonal_type;

    uint64 rank(
        const qgram_index_type& qgram_index,
        const uint32            n_queries,
        const query_iterator    queries,
        const index_iterator    indices);

    template <typename hits_iterator>
    void locate(
        const uint64    begin,
        const uint64    end,
        hits_iterator   hits);

    template <typename hits_iterator, typename output_iterator>
    void diagonals(
        const uint32            n_hits,
        const hits_iterator     hits,
              output_iterator   diags,
        const uint32            interval = 1);

    template <typename hits_iterator, typename output_iterator, typename count_iterator>
    uint32 merge(
        const uint32            interval,
        const uint32            n_hits,
        const hits_iterator     hits,
              output_iterator   merged_hits,
              count_iterator    merged_counts);

    const uint2* ranges() const { return nvbio::plain_view( m_ranges ); }

    const uint64* ranks() const { return nvbio::plain_view( m_slots ); }

    uint32                              m_n_queries;
    query_iterator                      m_queries;
    index_iterator                      m_indices;
    qgram_index_view                    m_qgram_index;
    uint64                              m_n_occurrences;
    thrust::host_vector<uint2>          m_ranges;
    thrust::host_vector<uint64>         m_slots;
    thrust::host_vector<diagonal_type>  m_diags;
};

template <typename qgram_index_type, typename query_iterator, typename index_iterator>
struct QGramFilter<device_tag, qgram_index_type, query_iterator, index_iterator>
{
    typedef device_tag          system_tag;

    typedef typename plain_view_subtype<const qgram_index_type>::type qgram_index_view;

    typedef typename qgram_index_type::coord_type coord_type;   

    typedef typename if_equal<coord_type, uint32, uint2,  uint4>::type  hit_type;
    typedef typename if_equal<coord_type, uint32, uint32, uint2>::type  diagonal_type;

    uint64 rank(
        const qgram_index_type& qgram_index,
        const uint32            n_queries,
        const query_iterator    queries,
        const index_iterator    indices);

    template <typename hits_iterator>
    void locate(
        const uint64            begin,
        const uint64            end,
        hits_iterator           hits);

    template <typename hits_iterator, typename output_iterator>
    void diagonals(
        const uint32            n_hits,
        const hits_iterator     hits,
              output_iterator   diags,
        const uint32            interval = 1);

    template <typename hits_iterator, typename output_iterator, typename count_iterator>
    uint32 merge(
        const uint32            interval,
        const uint32            n_hits,
        const hits_iterator     hits,
              output_iterator   merged_hits,
              count_iterator    merged_counts);

    const uint2* ranges() const { return nvbio::plain_view( m_ranges ); }

    const uint64* ranks() const { return nvbio::plain_view( m_slots ); }

    uint32                                  m_n_queries;
    query_iterator                          m_queries;
    index_iterator                          m_indices;
    qgram_index_view                        m_qgram_index;
    uint64                                  m_n_occurrences;
    thrust::device_vector<uint2>            m_ranges;
    thrust::device_vector<uint64>           m_slots;
    thrust::device_vector<diagonal_type>    m_diags;
    thrust::device_vector<uint8>            d_temp_storage;
};

template <typename qgram_index_type, typename query_iterator, typename index_iterator>
struct QGramFilterHost : public QGramFilter<host_tag, qgram_index_type, query_iterator, index_iterator> {};

template <typename qgram_index_type, typename query_iterator, typename index_iterator>
struct QGramFilterDevice : public QGramFilter<device_tag, qgram_index_type, query_iterator, index_iterator> {};


} // namespace nvbio

#include <nvbio/qgram/filter_inl.h>