ms_treecluster.hpp

/*
##############################################################################
# File: ms_treecluster.hpp                                                      #
# Mascot Parser toolkit                                                      #
# Utility functions for hierarchical clustering                              #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2012 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Source: parser/inc/ms_treecluster.hpp $
#    $Author: villek@matrixscience.com $ 
#      $Date: 2019-05-10 10:45:13 +0100 $ 
#  $Revision: 3770d1f7ee65bb20469e6c0ca909b2045b16fd74 | MSPARSER_REL_2_8_1-0-gea32989045 $
##############################################################################
*/

#ifndef MS_TREECLUSTER_HPP
#define MS_TREECLUSTER_HPP


#include <string>
#include <vector>


namespace matrix_science {


    class MS_MASCOTRESFILE_API ms_treecluster: public ms_errors
    {
    public:


        enum TREE_CLUSTER_DISTANCE {
            TCD_CORRELATION,                
            TCD_ABS_CORRELATION,            
            TCD_UNCENTERED_CORRELATION,     
            TCD_ABS_UNCENTERED_CORRELATION, 
            TCD_SPEARMANS_RANK_CORRELATION, 
            TCD_KENDALLS_TAU_CORRELATION,   
            TCD_EUCLIDEAN,                  
            TCD_CITY_BLOCK                  
        };

        ms_treecluster(int rows, int columns);

        ms_treecluster(const ms_treecluster& right);

        ~ms_treecluster();

#ifndef SWIG

        ms_treecluster& operator=(const ms_treecluster& right);
#endif

        void copyFrom(const ms_treecluster* right);

        void defaultValues();

        bool setRow(int row, std::vector< double > datarow, std::vector< int > maskrow);

        bool cluster(TREE_CLUSTER_DISTANCE tcd, 
                     ms_mascotresults::TREE_CLUSTER_METHOD tcm,
                     const std::vector< double > & weight,
                     std::vector< int >    &left, 
                     std::vector< int >    &right, 
                     std::vector< double > &distance, 
                     bool transpose = false );

    private:
        int numRows_;
        int numCols_;
        double ** data_;
        int    ** mask_;

        void freeMemory();

    }; // ms_treecluster // end of tools_group
} // matrix_science

#endif // MS_TREECLUSTER_HPP

/*------------------------------- End of File -------------------------------*/