/*
 * 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
 * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

// hello_world.cu
//

#include <stdio.h>
#include <stdlib.h>
#include <nvbio/basic/packed_vector.h>
#include <nvbio/basic/dna.h>
#include <nvbio/strings/infix.h>
#include <nvbio/strings/seeds.h>


using namespace nvbio;


// main test entry point
//
int main(int argc, char* argv[])
{
    // our hello world ASCII string
    const char dna_string[] = "ACGTTGCA";
    const uint32 len = (uint32)strlen( dna_string );

    // our DNA alphabet size
    const uint32 ALPHABET_SIZE = 2u;

    // instantiate a packed host vector
    nvbio::PackedVector<host_tag,ALPHABET_SIZE> h_dna( len );

    // pack our ASCII string
    string_to_dna(
        dna_string,         // begin iterator of our ASCII string
        h_dna.begin() );    // begin iterator of our output string

    // copy the packed vector to the device
    nvbio::PackedVector<device_tag,ALPHABET_SIZE> d_dna( h_dna );

    return 0;
}
