A library for working with phylogenetic and population genetic data.
v0.27.0
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) 2014-2022 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 <lczech@carnegiescience.edu>
23  Department of Plant Biology, Carnegie Institution For Science
24  260 Panama Street, Stanford, CA 94305, USA
25 */
26 
36 #include "genesis/utils/containers/dataframe.hpp"
37 #include "genesis/utils/containers/dataframe/operators.hpp"
38 #include "genesis/utils/containers/dataframe/reader.hpp"
39 #include "genesis/utils/containers/deref_iterator.hpp"
40 #include "genesis/utils/containers/filter_iterator.hpp"
41 #include "genesis/utils/containers/function_cache.hpp"
42 #include "genesis/utils/containers/hash_tuple.hpp"
43 #include "genesis/utils/containers/interval_tree/functions.hpp"
44 #include "genesis/utils/containers/interval_tree/fwd.hpp"
45 #include "genesis/utils/containers/interval_tree.hpp"
46 #include "genesis/utils/containers/interval_tree/interval.hpp"
47 #include "genesis/utils/containers/interval_tree/iterator.hpp"
48 #include "genesis/utils/containers/interval_tree/node.hpp"
49 #include "genesis/utils/containers/lambda_iterator.hpp"
50 #include "genesis/utils/containers/matrix/col.hpp"
51 #include "genesis/utils/containers/matrix.hpp"
52 #include "genesis/utils/containers/matrix/operators.hpp"
53 #include "genesis/utils/containers/matrix/reader.hpp"
54 #include "genesis/utils/containers/matrix/row.hpp"
55 #include "genesis/utils/containers/matrix/writer.hpp"
56 #include "genesis/utils/containers/mru_cache.hpp"
57 #include "genesis/utils/containers/optional.hpp"
58 #include "genesis/utils/containers/range.hpp"
59 #include "genesis/utils/containers/transform_iterator.hpp"
60 #include "genesis/utils/core/algorithm.hpp"
61 #include "genesis/utils/core/exception.hpp"
62 #include "genesis/utils/core/fs.hpp"
63 #include "genesis/utils/core/logging.hpp"
64 #include "genesis/utils/core/options.hpp"
65 #include "genesis/utils/core/std.hpp"
66 #include "genesis/utils/core/thread_pool.hpp"
67 #include "genesis/utils/core/version.hpp"
68 #include "genesis/utils/formats/bmp/writer.hpp"
69 #include "genesis/utils/formats/csv/input_iterator.hpp"
70 #include "genesis/utils/formats/csv/reader.hpp"
71 #include "genesis/utils/formats/json/document.hpp"
72 #include "genesis/utils/formats/json/iterator.hpp"
73 #include "genesis/utils/formats/json/reader.hpp"
74 #include "genesis/utils/formats/json/writer.hpp"
75 #include "genesis/utils/formats/nexus/block.hpp"
76 #include "genesis/utils/formats/nexus/document.hpp"
77 #include "genesis/utils/formats/nexus/taxa.hpp"
78 #include "genesis/utils/formats/nexus/trees.hpp"
79 #include "genesis/utils/formats/nexus/writer.hpp"
80 #include "genesis/utils/formats/svg/attributes.hpp"
81 #include "genesis/utils/formats/svg/color_bar.hpp"
82 #include "genesis/utils/formats/svg/definitions.hpp"
83 #include "genesis/utils/formats/svg/document.hpp"
84 #include "genesis/utils/formats/svg/gradient.hpp"
85 #include "genesis/utils/formats/svg/group.hpp"
86 #include "genesis/utils/formats/svg/helper.hpp"
87 #include "genesis/utils/formats/svg/image.hpp"
88 #include "genesis/utils/formats/svg/matrix.hpp"
89 #include "genesis/utils/formats/svg/object.hpp"
90 #include "genesis/utils/formats/svg/shapes.hpp"
91 #include "genesis/utils/formats/svg/svg.hpp"
92 #include "genesis/utils/formats/svg/text.hpp"
93 #include "genesis/utils/formats/xml/document.hpp"
94 #include "genesis/utils/formats/xml/helper.hpp"
95 #include "genesis/utils/formats/xml/writer.hpp"
96 #include "genesis/utils/io/base64.hpp"
97 #include "genesis/utils/io/base_input_source.hpp"
98 #include "genesis/utils/io/base_output_target.hpp"
99 #include "genesis/utils/io/deserializer.hpp"
100 #include "genesis/utils/io/file_input_source.hpp"
101 #include "genesis/utils/io/file_output_target.hpp"
102 #include "genesis/utils/io/gzip_block_ostream.hpp"
103 #include "genesis/utils/io/gzip.hpp"
104 #include "genesis/utils/io/gzip_input_source.hpp"
105 #include "genesis/utils/io/gzip_output_target.hpp"
106 #include "genesis/utils/io/gzip_stream.hpp"
107 #include "genesis/utils/io/input_buffer.hpp"
108 #include "genesis/utils/io/input_reader.hpp"
109 #include "genesis/utils/io/input_source.hpp"
110 #include "genesis/utils/io/input_stream.hpp"
111 #include "genesis/utils/io/output_stream.hpp"
112 #include "genesis/utils/io/output_target.hpp"
113 #include "genesis/utils/io/parser.hpp"
114 #include "genesis/utils/io/scanner.hpp"
115 #include "genesis/utils/io/serializer.hpp"
116 #include "genesis/utils/io/stream_input_source.hpp"
117 #include "genesis/utils/io/stream_output_target.hpp"
118 #include "genesis/utils/io/strict_fstream.hpp"
119 #include "genesis/utils/io/string_input_source.hpp"
120 #include "genesis/utils/io/string_output_target.hpp"
121 #include "genesis/utils/math/bitvector/helper.hpp"
122 #include "genesis/utils/math/bitvector.hpp"
123 #include "genesis/utils/math/bitvector/operators.hpp"
124 #include "genesis/utils/math/common.hpp"
125 #include "genesis/utils/math/distance.hpp"
126 #include "genesis/utils/math/euclidean_kmeans.hpp"
127 #include "genesis/utils/math/histogram/accumulator.hpp"
128 #include "genesis/utils/math/histogram/distances.hpp"
129 #include "genesis/utils/math/histogram.hpp"
130 #include "genesis/utils/math/histogram/operations.hpp"
131 #include "genesis/utils/math/histogram/operators.hpp"
132 #include "genesis/utils/math/histogram/stats.hpp"
133 #include "genesis/utils/math/kmeans.hpp"
134 #include "genesis/utils/math/matrix.hpp"
135 #include "genesis/utils/math/mds.hpp"
136 #include "genesis/utils/math/pca.hpp"
137 #include "genesis/utils/math/random.hpp"
138 #include "genesis/utils/math/range_minimum_query.hpp"
139 #include "genesis/utils/math/ranking.hpp"
140 #include "genesis/utils/math/regression/dataframe.hpp"
141 #include "genesis/utils/math/regression/factor.hpp"
142 #include "genesis/utils/math/regression/family.hpp"
143 #include "genesis/utils/math/regression/glm.hpp"
144 #include "genesis/utils/math/regression/helper.hpp"
145 #include "genesis/utils/math/regression/link.hpp"
146 #include "genesis/utils/math/regression/slr.hpp"
147 #include "genesis/utils/math/statistics.hpp"
148 #include "genesis/utils/math/twobit_vector/functions.hpp"
149 #include "genesis/utils/math/twobit_vector.hpp"
150 #include "genesis/utils/math/twobit_vector/iterator_deletions.hpp"
151 #include "genesis/utils/math/twobit_vector/iterator_insertions.hpp"
152 #include "genesis/utils/math/twobit_vector/iterator_substitutions.hpp"
153 #include "genesis/utils/text/char.hpp"
154 #include "genesis/utils/text/convert.hpp"
155 #include "genesis/utils/text/string.hpp"
156 #include "genesis/utils/text/style.hpp"
157 #include "genesis/utils/text/table.hpp"
158 #include "genesis/utils/tools/char_lookup.hpp"
159 #include "genesis/utils/tools/color/functions.hpp"
160 #include "genesis/utils/tools/color/helpers.hpp"
161 #include "genesis/utils/tools/color.hpp"
162 #include "genesis/utils/tools/color/list_diverging.hpp"
163 #include "genesis/utils/tools/color/list_misc.hpp"
164 #include "genesis/utils/tools/color/list_qualitative.hpp"
165 #include "genesis/utils/tools/color/list_sequential.hpp"
166 #include "genesis/utils/tools/color/map.hpp"
167 #include "genesis/utils/tools/color/names.hpp"
168 #include "genesis/utils/tools/color/normalization.hpp"
169 #include "genesis/utils/tools/color/norm_boundary.hpp"
170 #include "genesis/utils/tools/color/norm_diverging.hpp"
171 #include "genesis/utils/tools/color/norm_linear.hpp"
172 #include "genesis/utils/tools/color/norm_logarithmic.hpp"
173 #include "genesis/utils/tools/date_time.hpp"
174 #include "genesis/utils/tools/geodesy/functions.hpp"
175 #include "genesis/utils/tools/geodesy/geo_coordinate.hpp"
176 #include "genesis/utils/tools/hash/functions.hpp"
177 #include "genesis/utils/tools/hash/md5.hpp"
178 #include "genesis/utils/tools/hash/sha1.hpp"
179 #include "genesis/utils/tools/hash/sha256.hpp"
180 #include "genesis/utils/tools/tickmarks.hpp"
181 
182 #endif // include guard
factor.hpp
range_minimum_query.hpp
table.hpp
algorithm.hpp
Provides some valuable algorithms that are not part of the C++ 11 STL.
parser.hpp
twobit_vector.hpp
gzip_input_source.hpp
helper.hpp
helper.hpp
ranking.hpp
fs.hpp
Provides functions for accessing the file system.
writer.hpp
helper.hpp
input_reader.hpp
glm.hpp
functions.hpp
slr.hpp
date_time.hpp
Provides functions for date and time access.
functions.hpp
common.hpp
fwd.hpp
output_stream.hpp
geo_coordinate.hpp
shapes.hpp
block.hpp
base_input_source.hpp
map.hpp
random.hpp
histogram.hpp
Header of Histogram class.
pca.hpp
gzip.hpp
helpers.hpp
operators.hpp
Header of Histogram operator functions.
version.hpp
Some stuff that is totally not imporatant, but nice.
dataframe.hpp
filter_iterator.hpp
iterator_insertions.hpp
std.hpp
Provides some valuable additions to STD.
group.hpp
serializer.hpp
Header of Serializer and Deserializer class.
iterator_deletions.hpp
input_source.hpp
reader.hpp
trees.hpp
iterator_substitutions.hpp
helper.hpp
string.hpp
Provides some commonly used string utility functions.
input_stream.hpp
gzip_output_target.hpp
document.hpp
function_cache.hpp
distance.hpp
matrix.hpp
sha1.hpp
operations.hpp
Header of Histogram operations functions.
file_output_target.hpp
logging.hpp
Provides easy and fast logging functionality.
document.hpp
distances.hpp
Header of Histogram distance functions.
operators.hpp
gzip_stream.hpp
range.hpp
node.hpp
char_lookup.hpp
string_output_target.hpp
col.hpp
reader.hpp
matrix.hpp
writer.hpp
kmeans.hpp
accumulator.hpp
Header of Histogram Accumulator class.
interval_tree.hpp
gradient.hpp
taxa.hpp
norm_diverging.hpp
stats.hpp
Header of Histogram statistics functions.
list_sequential.hpp
gzip_block_ostream.hpp
names.hpp
document.hpp
row.hpp
family.hpp
statistics.hpp
mru_cache.hpp
definitions.hpp
md5.hpp
functions.hpp
Color operators and functions.
functions.hpp
convert.hpp
transform_iterator.hpp
image.hpp
list_misc.hpp
char.hpp
color.hpp
Header of Color class.
reader.hpp
norm_linear.hpp
color_bar.hpp
options.hpp
strict_fstream.hpp
writer.hpp
interval.hpp
base64.hpp
list_diverging.hpp
text.hpp
exception.hpp
iterator.hpp
tickmarks.hpp
svg.hpp
writer.hpp
attributes.hpp
reader.hpp
norm_boundary.hpp
file_input_source.hpp
operators.hpp
Matrix operators.
matrix.hpp
scanner.hpp
output_target.hpp
deserializer.hpp
Header of Serializer and Deserializer class.
functions.hpp
iterator.hpp
string_input_source.hpp
stream_output_target.hpp
bitvector.hpp
list_qualitative.hpp
input_iterator.hpp
document.hpp
A collection of classes for working with XML documents. See XmlDocument for more.
normalization.hpp
hash_tuple.hpp
euclidean_kmeans.hpp
thread_pool.hpp
input_buffer.hpp
object.hpp
stream_input_source.hpp
dataframe.hpp
base_output_target.hpp
style.hpp
deref_iterator.hpp
mds.hpp
writer.hpp
lambda_iterator.hpp
operators.hpp
norm_logarithmic.hpp
sha256.hpp
optional.hpp