A toolkit for working with phylogenetic data.
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signatures.hpp
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1 #ifndef GENESIS_SEQUENCE_FUNCTIONS_SIGNATURES_H_
2 #define GENESIS_SEQUENCE_FUNCTIONS_SIGNATURES_H_
3 
4 /*
5  Genesis - A toolkit for working with phylogenetic data.
6  Copyright (C) 2014-2017 Lucas Czech
7 
8  This program is free software: you can redistribute it and/or modify
9  it under the terms of the GNU General Public License as published by
10  the Free Software Foundation, either version 3 of the License, or
11  (at your option) any later version.
12 
13  This program is distributed in the hope that it will be useful,
14  but WITHOUT ANY WARRANTY; without even the implied warranty of
15  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16  GNU General Public License for more details.
17 
18  You should have received a copy of the GNU General Public License
19  along with this program. If not, see <http://www.gnu.org/licenses/>.
20 
21  Contact:
22  Lucas Czech <lucas.czech@h-its.org>
23  Exelixis Lab, Heidelberg Institute for Theoretical Studies
24  Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
25 */
26 
34 #include<string>
35 #include<vector>
36 
37 namespace genesis {
38 namespace sequence {
39 
40 // =================================================================================================
41 // Forwad Declarations
42 // =================================================================================================
43 
44 class Sequence;
45 class SequenceSet;
46 
47 // =================================================================================================
48 // K-mers
49 // =================================================================================================
50 
58 std::vector<size_t> kmer_counts( Sequence const& seq, size_t k );
59 
69 std::vector<size_t> kmer_counts( Sequence const& seq, size_t k, std::string const& alphabet );
70 
77 std::vector<std::string> kmer_list( size_t k, std::string const& alphabet );
78 
79 // =================================================================================================
80 // Signatures
81 // =================================================================================================
82 
86 std::string reverse_complement( std::string const& sequence );
87 
91 size_t kmer_reverse_complement_size( size_t k );
92 
97 std::vector<size_t> kmer_reverse_complement_indices( size_t k );
98 
99 std::vector<double> signature_frequencies( Sequence const& seq, size_t k );
100 
101 } // namespace sequence
102 } // namespace genesis
103 
104 #endif // include guard
std::string reverse_complement(std::string const &sequence)
Get the reverse complement of a sequences of ACGT characters.
Definition: signatures.cpp:238
std::vector< double > signature_frequencies(Sequence const &seq, size_t k)
Definition: signatures.cpp:323
std::vector< size_t > kmer_reverse_complement_indices(size_t k)
Get a map from indices of kmer_list() and kmer_counts() vectors to a smaller list of size kmer_revers...
Definition: signatures.cpp:272
size_t kmer_reverse_complement_size(size_t k)
Get the size needed to store reverse complement kmers.
Definition: signatures.cpp:312
std::vector< size_t > kmer_counts(Sequence const &seq, size_t k)
Count the occurences of k-mers of size k, for nucleic acids "ACGT".
Definition: signatures.cpp:49
std::vector< std::string > kmer_list(size_t k, std::string const &alphabet)
Return the list of all possible k-mers for a given k and alphabet.
Definition: signatures.cpp:189