<filename>src/libgwaspp/algorithms/computation_engine.cpp
/*
* Copyright (c) 2012, <NAME>
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met: 
*
* 1. Redistributions of source code must retain the above copyright notice, this
*    list of conditions and the following disclaimer. 
* 2. 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. 
*
* 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 THE COPYRIGHT OWNER OR CONTRIBUTORS 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.
*
* The views and conclusions contained in the software and documentation are those
* of the authors and should not be interpreted as representing official policies, 
* either expressed or implied, of the FreeBSD Project.
*/
#include "algorithms/computation_engine.h"

namespace libgwaspp {
namespace algorithms {

void compute( void ( *f )( void *, void * ), void *input, void *output ) {
    INIT_LAPSE_TIME;
    RECORD_START;
    BasicInput *bi = reinterpret_cast<BasicInput *>( input );

    auto_ptr<IndexedInput> idx_input( new IndexedInput( bi ) );

    int idx = 0;

    /**
    Convert Marker ids into table order row index
    */
    set<string>::const_iterator it = bi->marker_ids->begin(), end = bi->marker_ids->end();
    for( ; it != end; ++it ) {
        idx = bi->gd->getGenotypedMarkerIndex( *it );
        assert( idx != -1 );

        idx_input->midx->insert( idx );
    }

    /**
    Covert Individual ids into table order column index
    */
    it = bi->individual_ids->begin();
    end = bi->individual_ids->end();
    for( ; it != end; ++it )  {
        idx = bi->gd->getGenotypedIndividualIndex( *it );
        assert( idx != -1 );

        idx_input->iidx->insert( idx );
    }

    f(( void * ) bi, output );

    RECORD_STOP;
    PRINT_LAPSE(cout, "Total runtime: " );
    cout << endl;
}

void compute( void ( *f )(GeneticData *, ostream *), GeneticData *gd, ostream *out ) {
    INIT_LAPSE_TIME;
    RECORD_START;

    if( out == NULL ) {
        out = &cout;
    }

    f( gd, out );

    RECORD_STOP;
    PRINT_LAPSE( cout, "Total runtime: " );
    cout << endl;
}

}
}
