labels.hpp

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#ifndef GENESIS_SEQUENCE_FUNCTIONS_LABELS_H_
#define GENESIS_SEQUENCE_FUNCTIONS_LABELS_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2019 Lucas Czech and HITS gGmbH
 
    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 "genesis/utils/tools/hash/functions.hpp"
 
#include <string>
#include <utility>
#include <unordered_map>
#include <unordered_set>
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     Forwad Declarations
// =================================================================================================
 
class Sequence;
class SequenceSet;
 
// =================================================================================================
//     Helper Structs
// =================================================================================================
 
struct LabelAttributes
{
    std::string label;
    std::unordered_map<std::string, std::string> attributes;
};
 
// =================================================================================================
//     General
// =================================================================================================
 
Sequence const* find_sequence( SequenceSet const& set, std::string const& label );
 
std::unordered_set<std::string> labels( SequenceSet const& set );
 
std::pair<std::string, size_t> guess_sequence_abundance( Sequence const& sequence );
 
std::pair<std::string, size_t> guess_sequence_abundance( std::string const& label );
 
LabelAttributes label_attributes( Sequence const& sequence );
 
LabelAttributes label_attributes( std::string const& label );
 
// =================================================================================================
//     Uniqueness
// =================================================================================================
 
bool has_unique_labels( SequenceSet const& set, bool case_sensitive = true );
 
void relabel_with_hash( Sequence& seq, utils::HashingFunctions hash_function );
 
void relabel_with_hash( SequenceSet& set, utils::HashingFunctions hash_function );
 
// =================================================================================================
//     Validity
// =================================================================================================
 
bool is_valid_label(   std::string const& label );
 
bool has_valid_label(  Sequence const&    seq );
 
bool has_valid_labels( SequenceSet const& set );
 
std::string sanitize_label( std::string const& label );
 
void sanitize_label( Sequence&     seq );
 
void sanitize_labels( SequenceSet& set );
 
// =================================================================================================
//     Modifiers
// =================================================================================================
 
void filter_by_label_list(
    SequenceSet&                           set,
    std::unordered_set<std::string> const& labels,
    bool                                   invert = false
);
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard