A toolkit for working with phylogenetic data.
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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) 2014-2017 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 <iosfwd>
35 #include <string>
36 
37 namespace genesis {
38 namespace sequence {
39 
40 // =================================================================================================
41 // Forward Declarations
42 // =================================================================================================
43 
44 class SequenceSet;
45 
46 // =================================================================================================
47 // Phylip Writer
48 // =================================================================================================
49 
51 {
52 public:
53 
54  // ---------------------------------------------------------------------
55  // Constructor and Rule of Five
56  // ---------------------------------------------------------------------
57 
58  PhylipWriter() = default;
59  ~PhylipWriter() = default;
60 
61  PhylipWriter( PhylipWriter const& ) = default;
62  PhylipWriter( PhylipWriter&& ) = default;
63 
64  PhylipWriter& operator= ( PhylipWriter const& ) = default;
65  PhylipWriter& operator= ( PhylipWriter&& ) = default;
66 
67  // ---------------------------------------------------------------------
68  // Writing
69  // ---------------------------------------------------------------------
70 
71  // void to_stream_interleaved ( SequenceSet const& sset, std::ostream& os ) const;
72  // void to_stream_sequential ( SequenceSet const& sset, std::ostream& os ) const;
73 
74  void to_stream ( SequenceSet const& sset, std::ostream& os ) const;
75  void to_file ( SequenceSet const& sset, std::string const& fn ) const;
76  std::string to_string ( SequenceSet const& sset ) const;
77 
78  // ---------------------------------------------------------------------
79  // Properties
80  // ---------------------------------------------------------------------
81 
82  PhylipWriter& label_length( size_t value );
83  size_t label_length() const;
84 
85  PhylipWriter& line_length( size_t value );
86  size_t line_length() const;
87 
88  // ---------------------------------------------------------------------
89  // Members
90  // ---------------------------------------------------------------------
91 
92 private:
93 
94  size_t label_length_ = 0;
95  size_t line_length_ = 80;
96 
97 };
98 
99 } // namespace sequence
100 } // namespace genesis
101 
102 #endif // include guard
PhylipWriter & operator=(PhylipWriter const &)=default
size_t line_length() const
Get the current line length.
std::string to_string(SequenceSet const &sset) const
Return Sequences of a SequenceSet in form of a Phylip formatted string.
Store a set of Sequences.
void to_stream(SequenceSet const &sset, std::ostream &os) const
Write Sequences of a SequenceSet to a stream in Phylip format.
void to_file(SequenceSet const &sset, std::string const &fn) const
Write Sequences of a SequenceSet to a file in Phylip format.
size_t label_length() const
Return the currently set label length.