src/coalescecluster.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 COALESCECLUSTER_H
#define COALESCECLUSTER_H

#include "coalesceclusteri.h"

namespace Sleipnir {

class CCoalesceCluster : public CCoalesceClusterImpl {
public:
    bool Initialize( const CPCL& PCL, CCoalesceCluster& Pot, const std::vector<SCoalesceDataset>& vecsDatasets,
        std::set<std::pair<size_t, size_t> >& setpriiSeeds, const std::vector<float>& vecdSeed, size_t iPairs, float dPValue,
        float dProbability, size_t iThreads );
    void Subtract( CPCL& PCL, const CCoalesceCluster& Pot ) const;
    void Subtract( CCoalesceGeneScores& GeneScores ) const;
    bool SelectConditions( const CPCL& PCL, const CCoalesceCluster& Pot, size_t iThreads, float dPValue,
        float dZScore );
    bool SelectMotifs( const CCoalesceGroupHistograms& HistsCluster, const CCoalesceGroupHistograms& HistsPot,
        float dPValue, float dZScore, size_t iMaxMotifs, size_t iThreads,
        const CCoalesceMotifLibrary* pMotifs = NULL );
    bool SelectGenes( const CPCL& PCL, const CCoalesceGeneScores& GeneScores,
        const CCoalesceGroupHistograms& HistsCluster, const CCoalesceGroupHistograms& HistsPot,
        size_t iMinimum, size_t iThreads, CCoalesceCluster& Pot, float dProbability,
        const CCoalesceMotifLibrary* pMotifs = NULL );
    void CalculateHistograms( const CCoalesceGeneScores& GeneScores,
        CCoalesceGroupHistograms& HistogramsCluster, CCoalesceGroupHistograms* pHistogramsPot ) const;
    size_t Open( const std::string& strPCL, size_t iSkip, const CPCL& PCL,
        CCoalesceMotifLibrary* pMotifs = NULL );
    size_t Open( std::istream& istm, const CPCL& PCL, CCoalesceMotifLibrary* pMotifs = NULL );
    bool Open( const CHierarchy& Hierarchy, const std::vector<CCoalesceCluster>& vecClusters,
        const std::vector<std::string>& vecstrClusters, float dFraction, float dCutoff, size_t iCutoff,
        CCoalesceMotifLibrary* pMotifs = NULL );
    bool Save( const std::string& strDirectory, size_t iID, const CPCL& PCL,
        const CCoalesceMotifLibrary* pMotifs = NULL ) const;
    void Save( std::ostream& ostm, size_t iID, const CPCL& PCL, const CCoalesceMotifLibrary* pMotifs = NULL,
        float dCutoffPWMs = 0, float dPenaltyGap = 0, float dPenaltyMismatch = 0, bool fNoRCs = false ) const;
    float GetSimilarity( const CCoalesceCluster& Cluster, size_t iGenes, size_t iDatasets ) const;
    void Snapshot( const CCoalesceGeneScores& GeneScores, CCoalesceGroupHistograms& Histograms );
    bool LabelMotifs( const CCoalesceMotifLibrary& Motifs, SMotifMatch::EType eMatchType, float dPenaltyGap,
        float dPenaltyMismatch, float dPValue );

    bool IsConverged( ) {

        return ( m_setiHistory.find( GetHash( ) ) != m_setiHistory.end( ) ); }

    bool IsEmpty( ) const {

        return ( m_setiGenes.empty( ) || m_setiDatasets.empty( ) ); }

    void SetGenes( size_t iGenes ) {
        size_t  i;

        m_setiGenes.clear( );
        for( i = 0; i < iGenes; ++i )
            m_setiGenes.insert( i ); }

    const std::set<size_t>& GetGenes( ) const {

        return CCoalesceClusterImpl::GetGenes( ); }

    const std::set<size_t>& GetDatasets( ) const {

        return m_setiDatasets; }

    const std::set<SMotifMatch>& GetMotifs( ) const {

        return m_setsMotifs; }

    bool IsGene( size_t iGene ) const {

        return CCoalesceClusterImpl::IsGene( iGene ); }

    bool IsDataset( size_t iDataset ) const {

        return ( m_setiDatasets.find( iDataset ) != m_setiDatasets.end( ) ); }

    void RemoveGenes( const std::vector<size_t>& veciGenes ) {
        size_t  i;

        for( i = 0; i < veciGenes.size( ); ++i )
            m_setiGenes.erase( veciGenes[ i ] ); }
};

}

#endif // COALESCECLUSTER_H