A toolkit for working with phylogenetic data.
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utils.hpp
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1 #ifndef GENESIS_UTILS_H_
2 #define GENESIS_UTILS_H_
3 
4 /*
5  Genesis - A toolkit for working with phylogenetic data.
6  Copyright (C) 2014-2018 Lucas Czech and HITS gGmbH
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 
36 #include "genesis/utils/containers/dataframe.hpp"
37 #include "genesis/utils/containers/dataframe/reader.hpp"
38 #include "genesis/utils/containers/matrix/col.hpp"
39 #include "genesis/utils/containers/matrix.hpp"
40 #include "genesis/utils/containers/matrix/operators.hpp"
41 #include "genesis/utils/containers/matrix/reader.hpp"
42 #include "genesis/utils/containers/matrix/row.hpp"
43 #include "genesis/utils/containers/matrix/writer.hpp"
44 #include "genesis/utils/containers/mru_cache.hpp"
45 #include "genesis/utils/containers/sorted_vector.hpp"
46 #include "genesis/utils/containers/sorted_vector/operators.hpp"
47 #include "genesis/utils/core/algorithm.hpp"
48 #include "genesis/utils/core/fs.hpp"
49 #include "genesis/utils/core/indexed_list.hpp"
50 #include "genesis/utils/core/logging.hpp"
51 #include "genesis/utils/core/options.hpp"
52 #include "genesis/utils/core/range.hpp"
53 #include "genesis/utils/core/std.hpp"
54 #include "genesis/utils/core/version.hpp"
55 #include "genesis/utils/formats/bmp/writer.hpp"
56 #include "genesis/utils/formats/csv/reader.hpp"
57 #include "genesis/utils/formats/json/document.hpp"
58 #include "genesis/utils/formats/json/iterator.hpp"
59 #include "genesis/utils/formats/json/reader.hpp"
60 #include "genesis/utils/formats/json/writer.hpp"
61 #include "genesis/utils/formats/nexus/block.hpp"
62 #include "genesis/utils/formats/nexus/document.hpp"
63 #include "genesis/utils/formats/nexus/taxa.hpp"
64 #include "genesis/utils/formats/nexus/trees.hpp"
65 #include "genesis/utils/formats/nexus/writer.hpp"
66 #include "genesis/utils/formats/svg/attributes.hpp"
67 #include "genesis/utils/formats/svg/color_bar.hpp"
68 #include "genesis/utils/formats/svg/definitions.hpp"
69 #include "genesis/utils/formats/svg/document.hpp"
70 #include "genesis/utils/formats/svg/gradient.hpp"
71 #include "genesis/utils/formats/svg/group.hpp"
72 #include "genesis/utils/formats/svg/helper.hpp"
73 #include "genesis/utils/formats/svg/image.hpp"
74 #include "genesis/utils/formats/svg/object.hpp"
75 #include "genesis/utils/formats/svg/shapes.hpp"
76 #include "genesis/utils/formats/svg/svg.hpp"
77 #include "genesis/utils/formats/svg/text.hpp"
78 #include "genesis/utils/formats/xml/document.hpp"
79 #include "genesis/utils/formats/xml/helper.hpp"
80 #include "genesis/utils/formats/xml/writer.hpp"
81 #include "genesis/utils/io/input_buffer.hpp"
82 #include "genesis/utils/io/input_reader.hpp"
83 #include "genesis/utils/io/input_source.hpp"
84 #include "genesis/utils/io/input_stream.hpp"
85 #include "genesis/utils/io/output_stream.hpp"
86 #include "genesis/utils/io/parser.hpp"
87 #include "genesis/utils/io/scanner.hpp"
88 #include "genesis/utils/io/serializer.hpp"
89 #include "genesis/utils/math/bitvector.hpp"
90 #include "genesis/utils/math/bitvector/operators.hpp"
91 #include "genesis/utils/math/common.hpp"
92 #include "genesis/utils/math/euclidean_kmeans.hpp"
93 #include "genesis/utils/math/histogram/accumulator.hpp"
94 #include "genesis/utils/math/histogram/distances.hpp"
95 #include "genesis/utils/math/histogram.hpp"
96 #include "genesis/utils/math/histogram/operations.hpp"
97 #include "genesis/utils/math/histogram/operators.hpp"
98 #include "genesis/utils/math/histogram/stats.hpp"
99 #include "genesis/utils/math/kmeans.hpp"
100 #include "genesis/utils/math/matrix.hpp"
101 #include "genesis/utils/math/pca.hpp"
102 #include "genesis/utils/math/random.hpp"
103 #include "genesis/utils/math/range_minimum_query.hpp"
104 #include "genesis/utils/math/statistics.hpp"
105 #include "genesis/utils/math/twobit_vector/functions.hpp"
106 #include "genesis/utils/math/twobit_vector.hpp"
107 #include "genesis/utils/math/twobit_vector/iterator_deletions.hpp"
108 #include "genesis/utils/math/twobit_vector/iterator_insertions.hpp"
109 #include "genesis/utils/math/twobit_vector/iterator_substitutions.hpp"
110 #include "genesis/utils/text/char.hpp"
111 #include "genesis/utils/text/string.hpp"
112 #include "genesis/utils/text/style.hpp"
113 #include "genesis/utils/text/table.hpp"
114 #include "genesis/utils/tools/char_lookup.hpp"
115 #include "genesis/utils/tools/color/diverging_lists.hpp"
116 #include "genesis/utils/tools/color/functions.hpp"
117 #include "genesis/utils/tools/color/helpers.hpp"
118 #include "genesis/utils/tools/color.hpp"
119 #include "genesis/utils/tools/color/map.hpp"
120 #include "genesis/utils/tools/color/names.hpp"
121 #include "genesis/utils/tools/color/normalization.hpp"
122 #include "genesis/utils/tools/color/norm_boundary.hpp"
123 #include "genesis/utils/tools/color/norm_diverging.hpp"
124 #include "genesis/utils/tools/color/norm_linear.hpp"
125 #include "genesis/utils/tools/color/norm_logarithmic.hpp"
126 #include "genesis/utils/tools/color/qualitative_lists.hpp"
127 #include "genesis/utils/tools/color/sequential_lists.hpp"
128 #include "genesis/utils/tools/date_time.hpp"
129 #include "genesis/utils/tools/geodesy/functions.hpp"
130 #include "genesis/utils/tools/geodesy.hpp"
131 #include "genesis/utils/tools/hashing.hpp"
132 #include "genesis/utils/tools/md5.hpp"
133 #include "genesis/utils/tools/sha1.hpp"
134 #include "genesis/utils/tools/sha256.hpp"
135 #include "genesis/utils/tools/tickmarks.hpp"
136 
137 #endif // include guard
euclidean_kmeans.hpp
iterator_substitutions.hpp
iterator_insertions.hpp
algorithm.hpp
Provides some valuable algorithms that are not part of the C++ 11 STL.
histogram.hpp
Header of Histogram class.
output_stream.hpp
mru_cache.hpp
text.hpp
sorted_vector.hpp
operations.hpp
Header of Histogram operations functions.
input_source.hpp
color.hpp
Header of Color class.
std.hpp
Provides some valuable additions to STD.
operators.hpp
Matrix operators.
norm_diverging.hpp
iterator_deletions.hpp
serializer.hpp
Header of Serializer and Deserializer class.
input_buffer.hpp
operators.hpp
Header of Histogram operator functions.
stats.hpp
Header of Histogram statistics functions.
twobit_vector.hpp
norm_logarithmic.hpp
document.hpp
A collection of classes for working with XML documents. See XmlDocument for more. ...
functions.hpp
string.hpp
Provides some commonly used string utility functions.
fs.hpp
Provides functions for accessing the file system.
date_time.hpp
Provides functions for date and time access.
logging.hpp
Provides easy and fast logging functionality.
accumulator.hpp
Header of Histogram Accumulator class.
norm_linear.hpp
qualitative_lists.hpp
operators.hpp
distances.hpp
Header of Histogram distance functions.
color_bar.hpp
norm_boundary.hpp
char_lookup.hpp
functions.hpp
Color operators and functions.
range_minimum_query.hpp
indexed_list.hpp
Header of IndexedList class.
input_reader.hpp
sequential_lists.hpp
input_stream.hpp
version.hpp
Some stuff that is totally not imporatant, but nice.
diverging_lists.hpp