sequence/functions/entropy.hpp

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#ifndef GENESIS_SEQUENCE_FUNCTIONS_ENTROPY_H_
#define GENESIS_SEQUENCE_FUNCTIONS_ENTROPY_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2020 Lucas Czech
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/
 
#include <cstddef>     // size_t
#include <type_traits> // underlying_type_t
#include <string>
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     Forwad Declarations
// =================================================================================================
 
class Sequence;
class SiteCounts;
class SequenceSet;
 
// =================================================================================================
//     Entropy Options
// =================================================================================================
 
enum class SiteEntropyOptions : unsigned char
{
    kDefault     = 0,
 
    kIncludeGaps = 1,
 
    kWeighted    = 2,
 
    kNormalized  = 4
};
 
inline SiteEntropyOptions operator | ( SiteEntropyOptions lhs, SiteEntropyOptions rhs )
{
    using T = std::underlying_type< SiteEntropyOptions >::type;
    return static_cast< SiteEntropyOptions >(
        static_cast< T >( lhs ) | static_cast< T >( rhs )
    );
}
 
inline SiteEntropyOptions& operator |= ( SiteEntropyOptions& lhs, SiteEntropyOptions rhs )
{
    using T = std::underlying_type< SiteEntropyOptions >::type;
    lhs = static_cast< SiteEntropyOptions >(
        static_cast< T >( lhs ) | static_cast< T >( rhs )
    );
    return lhs;
}
 
inline bool operator & ( SiteEntropyOptions lhs, SiteEntropyOptions rhs )
{
    using T = std::underlying_type< SiteEntropyOptions >::type;
    return static_cast< T >( lhs ) & static_cast< T >( rhs );
}
 
// =================================================================================================
//     Per Site Entropy and Information
// =================================================================================================
 
double site_entropy(
    SiteCounts const&     counts,
    size_t                site_index,
    SiteEntropyOptions    options = SiteEntropyOptions::kDefault
);
 
double site_information(
    SiteCounts const&     counts,
    size_t                site_index,
    bool                  use_small_sample_correction = false,
    SiteEntropyOptions    options = SiteEntropyOptions::kDefault
);
 
// =================================================================================================
//     Total Entropy and Information
// =================================================================================================
 
double absolute_entropy(
    SiteCounts const&     counts,
    SiteEntropyOptions    per_site_options = SiteEntropyOptions::kDefault
);
 
double average_entropy(
    SiteCounts const&     counts,
    bool                  only_determined_sites = false,
    SiteEntropyOptions    per_site_options = SiteEntropyOptions::kDefault
);
 
double absolute_information(
    SiteCounts const&     counts,
    bool                  use_small_sample_correction = false,
    SiteEntropyOptions    per_site_options = SiteEntropyOptions::kDefault
);
 
double average_information(
    SiteCounts const&     counts,
    bool                  only_determined_sites = false,
    bool                  use_small_sample_correction = false,
    SiteEntropyOptions    per_site_options = SiteEntropyOptions::kDefault
);
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard