src/compactmatrix.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 COMPACTMATRIX_H
#define COMPACTMATRIX_H

#include "compactmatrixi.h"

namespace Sleipnir {

class CCompactMatrix : CCompactMatrixImpl {
public:
    bool Open( std::istream& istm );
    const unsigned char* Open( const unsigned char* pbData );
    void Save( std::ostream& ostm ) const;

    void Randomize( ) {

        if( m_aiData )
            std::random_shuffle( m_aiData, m_aiData + CountWords( ) ); }

    void Set( size_t iY, size_t iX, unsigned char cValue ) {

        if( iX == iY )
            return;

        HalfIndex( iY, iX );
        CCompactMatrixBase::Set( iY, iX, cValue ); }

    void Initialize( size_t iSize, unsigned char cValues, bool fClear ) {

        m_iSize = (uint32_t)iSize;
        return CCompactMatrixBase::Initialize( cValues, fClear ); }

    size_t GetSize( ) const {

        return m_iSize; }

    unsigned char Get( size_t iY, size_t iX ) const {

        if( iX == iY )
            return 0;

        HalfIndex( iY, iX );
        return CCompactMatrixBase::Get( iY, iX ); }
};

class CCompactFullMatrix : CCompactFullMatrixImpl {
public:
    void Initialize( size_t iRows, size_t iColumns, unsigned char cValues, bool fClear ) {

        m_iRows = (uint32_t)iRows;
        m_iColumns = (uint32_t)iColumns;
        CCompactMatrixBase::Initialize( cValues, fClear ); }

    size_t GetRows( ) const {

        return m_iRows; }

    size_t GetColumns( ) const {

        return m_iColumns; }

    unsigned char Get( size_t iY, size_t iX ) const {

        return CCompactMatrixBase::Get( iY, iX ); }

    void Set( size_t iY, size_t iX, unsigned char cValue ) {

        CCompactMatrixBase::Set( iY, iX, cValue ); }
};

}

#endif // COMPACTMATRIX_H