src/pst.cpp

/*****************************************************************************
* This file is provided under the Creative Commons Attribution 3.0 license.
*
* You are free to share, copy, distribute, transmit, or adapt this work
* PROVIDED THAT you attribute the work to the authors listed below.
* For more information, please see the following web page:
* http://creativecommons.org/licenses/by/3.0/
*
* This file is a component of the Sleipnir library for functional genomics,
* authored by:
* Curtis Huttenhower (chuttenh@princeton.edu)
* Mark Schroeder
* Maria D. Chikina
* Olga G. Troyanskaya (ogt@princeton.edu, primary contact)
*
* If you use this library, the included executable tools, or any related
* code in your work, please cite the following publication:
* Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, and
* Olga G. Troyanskaya.
* "The Sleipnir library for computational functional genomics"
*****************************************************************************/
#include "stdafx.h"
#include "pst.h"
#include "coalescemotifs.h"

namespace Sleipnir {

struct SSortRCs {
    bool operator()( const string& strOne, const string& strTwo ) const {

        return ( strOne.length( ) > strTwo.length( ) ); }
};

void CPST::RemoveRCs( float dPenaltyGap, float dPenaltyMismatch, CPST& PSTOut ) const {
    size_t          i;
    string          str;
    vector<string>  vecstrAdd;
    float           dOne, dTwo;
    int             iOne, iTwo;

    CPSTImpl::RemoveRCs( m_sRoot, 1.0f / m_iArity, str, vecstrAdd );
    if( vecstrAdd.empty( ) )
        return;

    sort( vecstrAdd.begin( ), vecstrAdd.end( ), SSortRCs( ) );
    PSTOut.Add( vecstrAdd[ 0 ], 0 );
    for( i = 1; i < vecstrAdd.size( ); ++i ) {
        dOne = PSTOut.Align( vecstrAdd[ i ], dPenaltyGap, dPenaltyMismatch, FLT_MAX, iOne );
        dTwo = PSTOut.Align( str = CCoalesceMotifLibrary::GetReverseComplement( vecstrAdd[ i ] ),
            dPenaltyGap, dPenaltyMismatch, FLT_MAX, iTwo );
        if( dTwo < dOne )
            PSTOut.Add( str, iTwo );
        else
            PSTOut.Add( vecstrAdd[ i ], iOne ); } }

}