src/svmi.h

/*****************************************************************************
* 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"
*****************************************************************************/
#ifndef SVMI_H
#define SVMI_H

namespace SVMPerf {

extern "C" {
#undef int64_t
#include <svm_light/svm_common.h>
}

}
using namespace SVMPerf;

namespace Sleipnir {

class CDat;
class CDataPair;
class CGenes;
class CPCL;
class CPCLSet;
class IDataset;

class CSVMImpl {
protected:
    static const size_t c_iWords    = 512;

    struct SLearn : LEARN_PARM {
        SLearn( );
    };

    struct SKernel : KERNEL_PARM {
        SKernel( );
    };

    struct SData {
        enum {
            EPCL,
            EPCLs,
            EData,
            EFile
        }   m_eType;
        union {
            const CPCLSet*  m_pPCLs;
            const IDataset* m_pData;
            const char*     m_szFile;
            const CPCL*     m_pPCL;
        }   m_uData;
        union {
            const CDataPair*    m_pAnswers;
            const CGenes*       m_pGenes;
        }   m_uAnswers;
        const CGenes*   m_pNegative;
    };

    static SVMPerf::WORD    s_asWords[ c_iWords ];

    CSVMImpl( );
    ~CSVMImpl( );

    void Reset( bool, bool, bool );
    bool Initialize( const SData& );
    bool Evaluate( const SData&, const CGenes*, CDat& ) const;
    bool EvaluateFile( const char*, CDat& ) const;
    bool Learn( const SData& );
    size_t GetWords( const SData& ) const;
    DOC* CreateDoc( const SData&, size_t, size_t, size_t ) const;
    DOC* CreateDoc( const SData&, size_t ) const;

    MODEL*      m_pModel;
    DOC**       m_apDocs;
    uint32_t    m_iDocs;
    uint32_t    m_iWords;
    double*     m_adLabels;
    double*     m_adAlphas;
    size_t      m_iAlphas;
    SLearn      m_sLearn;
    SKernel     m_sKernel;
};

}

#endif // SVMI_H