src/clusthierarchical.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 CLUSHIERARCHICAL_H
#define CLUSHIERARCHICAL_H

#include "clusthierarchicali.h"

namespace Sleipnir {

class CPCL;
class IMeasure;

class CHierarchy : public CHierarchyImpl {
public:
    CHierarchy( size_t iID, float dSimilarity, const CHierarchy* pLeft, const CHierarchy* pRight );

    void GetGenes( std::vector<size_t>& veciGenes ) const;
    float SortChildren( const std::vector<float>& vecdScores );

    void Save( std::ostream& ostm, size_t iGenes,
        const std::vector<std::string>* pvecstrGenes = NULL ) const {
        size_t  i;

        for( i = 0; ( i + 1 ) < iGenes; ++i )
            CHierarchyImpl::Save( ostm, i, pvecstrGenes ); }

    void Destroy( ) {

        delete this; }

    float GetSimilarity( ) const {

        return m_dScore; }

    bool IsGene( ) const {

        return CHierarchyImpl::IsGene( ); }

    size_t GetID( ) const {

        return m_iID; }

    const CHierarchy& Get( bool fRight ) const {

        return *( fRight ? m_pRight : m_pLeft ); }

    size_t GetWeight( ) const {

        return m_iWeight; }
};

class CClustHierarchical : CClustHierarchicalImpl {
public:
    static CHierarchy* Cluster( const CDistanceMatrix& MatSimilarities );
    static CHierarchy* Cluster( const CDistanceMatrix& MatSimilarities,
        const std::vector<bool>& vecfIncluded );
};

}

#endif // CLUSHIERARCHICAL_H