src/clusthierarchicali.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 CLUSHIERARCHICALI_H
#define CLUSHIERARCHICALI_H

#include <string>
#include <vector>

#include "fullmatrix.h"
#include "halfmatrix.h"

namespace Sleipnir {

class CHierarchy;

class CHierarchyImpl {
protected:
    ~CHierarchyImpl( );

    std::string GetSave( const std::vector<std::string>* = NULL ) const;
    bool Save( std::ostream&, size_t, const std::vector<std::string>* ) const;

    bool IsGene( ) const {

        return !( m_pLeft && m_pRight ); }

    size_t              m_iID;
    size_t              m_iWeight;
    float               m_dScore;
    const CHierarchy*   m_pLeft;
    const CHierarchy*   m_pRight;
};

class CClustHierarchicalImpl {
protected:

    static CHierarchy* Cluster( const CDistanceMatrix&, const std::vector<bool>* = NULL );
    static CHierarchy* ConstructHierarchy( const std::vector<size_t>&, const std::vector<size_t>&,
        const std::vector<float>&, size_t );
    static void UpdateDistances( size_t, size_t, CDistanceMatrix&, size_t, size_t, std::vector<float>&,
        std::vector<size_t>& );

    static void AssertParentage( std::vector<size_t>& veciChildren, std::vector<size_t>& veciChild1,
        std::vector<size_t>& veciChild2, size_t iChild, size_t iParent ) {

        veciChildren[ iParent ] += veciChildren[ iChild ];
        iParent -= veciChild1.size( );
        veciChild2[ iParent ] = veciChild1[ iParent ];
        veciChild1[ iParent ] = iChild; }
};

}

#endif // CLUSHIERARCHICALI_H