A toolkit for working with phylogenetic data.
v0.24.0
phylip_writer.hpp
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1 #ifndef GENESIS_SEQUENCE_FORMATS_PHYLIP_WRITER_H_
2 #define GENESIS_SEQUENCE_FORMATS_PHYLIP_WRITER_H_
3 
4 /*
5  Genesis - A toolkit for working with phylogenetic data.
6  Copyright (C) 2014-2020 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 
35 
36 #include <iosfwd>
37 #include <string>
38 
39 namespace genesis {
40 namespace sequence {
41 
42 // =================================================================================================
43 // Forward Declarations
44 // =================================================================================================
45 
46 class SequenceSet;
47 
48 // =================================================================================================
49 // Phylip Writer
50 // =================================================================================================
51 
53 {
54 public:
55 
56  // ---------------------------------------------------------------------
57  // Constructor and Rule of Five
58  // ---------------------------------------------------------------------
59 
60  PhylipWriter() = default;
61  ~PhylipWriter() = default;
62 
63  PhylipWriter( PhylipWriter const& ) = default;
64  PhylipWriter( PhylipWriter&& ) = default;
65 
66  PhylipWriter& operator= ( PhylipWriter const& ) = default;
67  PhylipWriter& operator= ( PhylipWriter&& ) = default;
68 
69  // ---------------------------------------------------------------------
70  // Writing
71  // ---------------------------------------------------------------------
72 
73  // void to_stream_interleaved ( SequenceSet const& sequence_set, std::ostream& os ) const;
74  // void to_stream_sequential ( SequenceSet const& sequence_set, std::ostream& os ) const;
75 
82  void write( SequenceSet const& sequence_set, std::shared_ptr<utils::BaseOutputTarget> target ) const;
83 
84  // ---------------------------------------------------------------------
85  // Properties
86  // ---------------------------------------------------------------------
87 
103  PhylipWriter& label_length( size_t value );
104 
110  size_t label_length() const;
111 
119  PhylipWriter& line_length( size_t value );
120 
126  size_t line_length() const;
127 
128  // ---------------------------------------------------------------------
129  // Members
130  // ---------------------------------------------------------------------
131 
132 private:
133 
134  size_t label_length_ = 0;
135  size_t line_length_ = 80;
136 
137 };
138 
139 } // namespace sequence
140 } // namespace genesis
141 
142 #endif // include guard
PhylipWriter & operator=(PhylipWriter const &)=default
size_t line_length() const
Get the current line length.
Container namespace for all symbols of genesis in order to keep them separate when used as a library...
size_t label_length() const
Return the currently set label length.
Store a set of Sequences.
void write(SequenceSet const &sequence_set, std::shared_ptr< utils::BaseOutputTarget > target) const
Write a SequenceSet to an output target, using the Phylip format.