File List

Here is a list of all files with brief descriptions:

accumulator.cpp	Implementation of Histogram Accumulator class
accumulator.hpp	Header of Histogram Accumulator class
af_spectrum.cpp
af_spectrum.hpp
afs_estimate.cpp
afs_estimate.hpp
algorithm.hpp	Provides some valuable algorithms that are not part of the C++ 11 STL
attributes.cpp
attributes.hpp
balances.cpp
balances.hpp
base64.cpp
base64.hpp
base_counts.hpp
base_input_source.hpp
base_output_target.hpp
base_window_iterator.hpp
bed_reader.cpp
bed_reader.hpp
bipartition.hpp
bitmap.cpp
bitmap.hpp
bitvector.cpp	Implementation of bitvector functions
bitvector.hpp
block.cpp
block.hpp
broker.cpp	Implementation of NewickBroker class
broker.hpp
char.cpp	Implementation of string utility functions
char.hpp
char_lookup.hpp
circular_layout.cpp
circular_layout.hpp
codes.cpp
codes.hpp
cog.cpp
cog.hpp
col.hpp
color.cpp
color.hpp	Header of Color class
color_bar.cpp
color_bar.hpp
color_writer_plugin.hpp
newick/color_writer_plugin.hpp
phyloxml/color_writer_plugin.hpp
common.cpp
common.hpp
compact.cpp
compact.hpp
consensus.cpp
consensus.hpp
convert.cpp
convert.hpp
counts.cpp
counts.hpp
dataframe.cpp
containers/dataframe.hpp
math/regression/dataframe.hpp
date_time.cpp	Implementation of date and time functions
date_time.hpp	Provides functions for date and time access
definitions.hpp
deref_iterator.hpp
deserializer.hpp	Header of Serializer and Deserializer class
detailed.cpp
detailed.hpp
distance.cpp
distance.hpp
placement/function/distances.cpp
tree/common_tree/distances.cpp	Implementation of CommonTree distance methods
tree/function/distances.cpp	Implementation of Tree distance methods
utils/math/histogram/distances.cpp	Implementation of Histogram distance functions
placement/function/distances.hpp
tree/common_tree/distances.hpp	Header of CommonTree distance methods
tree/function/distances.hpp	Header of Tree distance methods
utils/math/histogram/distances.hpp	Header of Histogram distance functions
distributions.cpp
distributions.hpp
diversity.cpp
diversity.hpp
json/document.cpp
nexus/document.cpp
svg/document.cpp
xml/document.cpp	Implementation of XML document functions
json/document.hpp
nexus/document.hpp
svg/document.hpp
xml/document.hpp	A collection of classes for working with XML documents. See XmlDocument for more
edge.hpp
placement/formats/edge_color.cpp
tree/common_tree/edge_color.cpp
placement/formats/edge_color.hpp
tree/common_tree/edge_color.hpp
edge_data.hpp
element.hpp
placement/function/emd.cpp
tree/mass_tree/emd.cpp
placement/function/emd.hpp
tree/mass_tree/emd.hpp
sequence/functions/entropy.cpp
taxonomy/functions/entropy.cpp
sequence/functions/entropy.hpp
taxonomy/functions/entropy.hpp
entropy_data.hpp
epca.cpp
epca.hpp
euclidean_kmeans.cpp
euclidean_kmeans.hpp
eulertour.hpp
exception.hpp
factor.hpp
family.hpp
fasta_input_iterator.hpp
fasta_output_iterator.hpp
fasta_reader.cpp
fasta_reader.hpp
fasta_writer.cpp
fasta_writer.hpp
fastq_input_iterator.hpp
fastq_output_iterator.hpp
fastq_reader.cpp
fastq_reader.hpp
fastq_writer.cpp
fastq_writer.hpp
file_input_source.hpp
file_output_target.hpp
filter_iterator.hpp
filter_transform.cpp
filter_transform.hpp
fs.cpp	Implementation of file system functions
fs.hpp	Provides functions for accessing the file system
function_cache.hpp
placement/function/functions.cpp	Implementation of the Placement Functions
placement/simulator/functions.cpp
population/functions/functions.cpp
sequence/functions/functions.cpp
tree/bipartition/functions.cpp
tree/common_tree/functions.cpp	Implementation of Common Tree functions
tree/drawing/functions.cpp
tree/function/functions.cpp
tree/mass_tree/functions.cpp
utils/math/twobit_vector/functions.cpp
utils/tools/color/functions.cpp	Color operators and functions
utils/tools/geodesy/functions.cpp
utils/tools/hash/functions.cpp
placement/function/functions.hpp	Provides functions for working with Placements and Pqueries
placement/simulator/functions.hpp
population/functions/functions.hpp
population/window/functions.hpp
sequence/functions/functions.hpp
tree/bipartition/functions.hpp
tree/common_tree/functions.hpp	CommonTree functions
tree/drawing/functions.hpp
tree/function/functions.hpp
tree/mass_tree/functions.hpp
utils/containers/interval_tree/functions.hpp
utils/math/twobit_vector/functions.hpp
utils/tools/color/functions.hpp	Color operators and functions
utils/tools/geodesy/functions.hpp
utils/tools/hash/functions.hpp
fwd.hpp
genesis.hpp
genome_heatmap.cpp
genome_heatmap.hpp
functions/genome_locus.hpp
genome_locus.hpp
genome_region.cpp
functions/genome_region.hpp
genome_region.hpp
genome_region_list.hpp
geo_coordinate.hpp
gff_reader.cpp
gff_reader.hpp
glm.cpp
glm.hpp
gradient.cpp
gradient.hpp
group.cpp
group.hpp
gzip.cpp
gzip.hpp
gzip_block_ostream.cpp
gzip_block_ostream.hpp
gzip_input_source.cpp
gzip_input_source.hpp
gzip_output_target.hpp
gzip_stream.cpp
gzip_stream.hpp
hash_tuple.hpp
heat_tree.cpp
heat_tree.hpp
heatmap_colorization.cpp
heatmap_colorization.hpp
heatmap_matrix.hpp
placement/function/helper.cpp	Implementation of the Placement Functions
utils/formats/xml/helper.cpp
utils/math/bitvector/helper.cpp
utils/math/regression/helper.cpp
placement/function/helper.hpp
utils/formats/svg/helper.hpp
utils/formats/xml/helper.hpp
utils/math/bitvector/helper.hpp
utils/math/regression/helper.hpp
helpers.cpp
helpers.hpp
histogram.cpp	Implementation of Histogram class
histogram.hpp	Header of Histogram class
hts_file.cpp
hts_file.hpp
image.cpp
image.hpp
indexed_newick_reader.cpp	Implementation of NewickBroker class
indexed_newick_reader.hpp
input_buffer.hpp
tree/formats/newick/input_iterator.hpp
utils/formats/csv/input_iterator.hpp
input_reader.hpp
input_source.hpp
input_stream.cpp
input_stream.hpp
interval.hpp
interval_tree.hpp
containers/interval_tree/iterator.hpp
formats/json/iterator.hpp
iterator_deletions.hpp
iterator_insertions.hpp
iterator_substitutions.hpp
jplace_reader.cpp
jplace_reader.hpp
jplace_writer.cpp
jplace_writer.hpp
keyed_newick_reader.cpp	Implementation of NewickBroker class
keyed_newick_reader.hpp
kmeans.cpp
tree/mass_tree/kmeans.hpp
utils/math/kmeans.hpp
labels.cpp
labels.hpp
lambda_iterator.hpp
layout_base.cpp
layout_base.hpp
layout_tree.hpp
lca_lookup.cpp
lca_lookup.hpp
taxonomy/iterator/levelorder.hpp
tree/iterator/levelorder.hpp
tree/tree/link.hpp
utils/math/regression/link.hpp
list_diverging.cpp
list_diverging.hpp
list_misc.cpp
list_misc.hpp
list_qualitative.cpp
list_qualitative.hpp
list_sequential.cpp
list_sequential.hpp
logging.cpp	Implementation of Logging functions
logging.hpp	Provides easy and fast logging functionality
placement/function/manipulation.cpp
tree/function/manipulation.cpp
placement/function/manipulation.hpp
tree/function/manipulation.hpp
map.cpp
map.hpp
masses.cpp	Implementation of the Placement Functions
masses.hpp
formats/svg/matrix.cpp
math/matrix.cpp
containers/matrix.hpp
formats/svg/matrix.hpp
math/matrix.hpp
md5.cpp
md5.hpp
mds.cpp
mds.hpp
measures.cpp	Implementation of PlacementMeasures class
measures.hpp	Header for Placement Measures functions
mru_cache.hpp
name.hpp
names.cpp
names.hpp
ncbi.cpp
ncbi.hpp
nested.cpp	Implementation of Taxonomy class
nested.hpp
placement/formats/newick_reader.hpp
tree/common_tree/newick_reader.hpp
placement/formats/newick_writer.hpp
tree/common_tree/newick_writer.hpp
nhd.cpp
nhd.hpp
tree/tree/node.hpp
utils/containers/interval_tree/node.hpp
node_data.hpp
node_links.hpp
norm_boundary.hpp
norm_diverging.hpp
norm_linear.hpp
norm_logarithmic.hpp
normalization.hpp
object.hpp
operations.cpp	Implementation of Histogram operations functions
operations.hpp	Header of Histogram operations functions
placement/function/operators.cpp
tree/common_tree/operators.cpp
tree/function/operators.cpp	Implementation of Tree operator functions
utils/containers/dataframe/operators.cpp
utils/containers/matrix/operators.cpp
utils/math/bitvector/operators.cpp
utils/math/histogram/operators.cpp	Implementation of Histogram operator functions
placement/function/operators.hpp
taxonomy/functions/operators.hpp
tree/common_tree/operators.hpp
tree/function/operators.hpp	Tree operator functions
utils/containers/dataframe/operators.hpp
utils/containers/matrix/operators.hpp	Matrix operators
utils/math/bitvector/operators.hpp
utils/math/histogram/operators.hpp	Header of Histogram operator functions
optional.hpp
options.cpp	Implementation of Options members
options.hpp
output_stream.hpp
output_target.hpp
parser.cpp
parser.hpp
path.hpp
path_set.hpp
pca.cpp
pca.hpp
phylip_reader.cpp
phylip_reader.hpp
phylip_writer.cpp
phylip_writer.hpp
phylo_factor.cpp
phylo_factor.hpp
phylo_factor_colors.cpp
phylo_factor_colors.hpp
phylo_ilr.cpp
phylo_ilr.hpp
phyloxml_writer.hpp
placement/pquery/placement.hpp	Header of PqueryPlacement class
placement.hpp
placement_tree.hpp
plain.hpp	Header of PqueryPlain class
population.hpp
taxonomy/iterator/postorder.hpp
tree/iterator/postorder.hpp
pquery.cpp	Implementation of Pquery class
pquery.hpp
taxonomy/iterator/preorder.hpp
tree/iterator/preorder.hpp
quality.cpp
quality.hpp
random.cpp
random.hpp
range.hpp
range_minimum_query.cpp
range_minimum_query.hpp
ranking.hpp
ranks.cpp
ranks.hpp
tree/formats/newick/reader.cpp
utils/formats/csv/reader.cpp
utils/formats/json/reader.cpp
tree/formats/newick/reader.hpp
utils/containers/dataframe/reader.hpp
utils/containers/matrix/reader.hpp
utils/formats/csv/reader.hpp
utils/formats/json/reader.hpp
rectangular_layout.cpp
rectangular_layout.hpp
region_window_iterator.hpp
rf.cpp
rf.hpp
row.hpp
sam_flags.cpp
sam_flags.hpp
sam_variant_input_iterator.cpp
sam_variant_input_iterator.hpp
sample.cpp	Implementation of Sample class
sample.hpp
sample_set.cpp
function/sample_set.hpp
sample_set.hpp
scanner.hpp
sequence/sequence.hpp
sequence.hpp
sequence_set.cpp	Implementation of SequenceSet class
sequence_set.hpp
serializer.cpp	Implementation of SampleSerializer class
placement/formats/serializer.hpp	Header of SampleSerializer class
utils/io/serializer.hpp	Header of Serializer and Deserializer class
sha1.cpp
sha1.hpp
sha256.cpp
sha256.hpp
shapes.cpp
shapes.hpp
signature_specifications.cpp
signature_specifications.hpp
signatures.cpp
signatures.hpp
simple.cpp
simple.hpp
simple_pileup_common.cpp
simple_pileup_common.hpp
simple_pileup_input_iterator.hpp
simple_pileup_reader.cpp
simple_pileup_reader.hpp
simple_reader.hpp
simple_tree.hpp
simple_writer.hpp
simulator.cpp	Implementation of Placement Simulator class
simulator.hpp
sliding_interval_window_iterator.hpp
sliding_variants_window_iterator.hpp
sliding_window_generator.hpp
slr.hpp
squash_clustering.cpp
squash_clustering.hpp
statistics.hpp
sequence/functions/stats.cpp
utils/math/histogram/stats.cpp	Implementation of Histogram statistics functions
sequence/functions/stats.hpp
utils/math/histogram/stats.hpp	Header of Histogram statistics functions
std.hpp	Provides some valuable additions to STD
stream_input_source.hpp
stream_output_target.hpp
strict_fstream.cpp
strict_fstream.hpp
string.cpp	Implementation of string utility functions
string.hpp	Provides some commonly used string utility functions
string_input_source.hpp
string_output_target.hpp
structure.cpp
structure.hpp
style.cpp
style.hpp
subtree.hpp
svg.hpp
sync_common.cpp
sync_common.hpp
sync_input_iterator.hpp
sync_reader.cpp
sync_reader.hpp
tree/printer/table.cpp
utils/text/table.cpp
tree/printer/table.hpp
utils/text/table.hpp
taxa.hpp
taxon.cpp	Implementation of Taxon class
taxon.hpp
taxon_data.hpp
functions/taxonomy.cpp
taxonomy.cpp	Implementation of Taxonomy class
taxonomy/functions/taxonomy.hpp
taxonomy/taxonomy.hpp
taxonomy.hpp
taxonomy_reader.cpp
taxonomy_reader.hpp
taxonomy_writer.cpp
taxonomy_writer.hpp
taxopath.cpp
functions/taxopath.hpp
taxopath.hpp
taxopath_generator.cpp	Implementation of TaxopathGenerator class
taxopath_generator.hpp
taxopath_parser.cpp	Implementation of TaxopathParser class
taxopath_parser.hpp
text.cpp
text.hpp
thread_pool.hpp
tickmarks.cpp
tickmarks.hpp
transform_iterator.hpp
placement/function/tree.cpp
taxonomy/functions/tree.cpp
tree/tree.cpp	Implementation of Tree class
placement/function/tree.hpp
taxonomy/functions/tree.hpp
tree/attribute_tree/tree.hpp
tree/common_tree/tree.hpp
tree/mass_tree/tree.hpp
tree/tree.hpp	Header of Tree class
tree.hpp
tree_set.cpp
function/tree_set.hpp
tree_set.hpp
trees.hpp
twobit_vector.cpp
twobit_vector.hpp
type_traits.hpp
utils.hpp
variant.hpp
variant_input_iterator.cpp
variant_input_iterator.hpp
variant_parallel_input_iterator.cpp
variant_parallel_input_iterator.hpp
variant_window_iterator.hpp
vcf_common.cpp
vcf_common.hpp
vcf_format_iterator.cpp
vcf_format_iterator.hpp
vcf_header.cpp
vcf_header.hpp
vcf_input_iterator.cpp
vcf_input_iterator.hpp
vcf_record.cpp
vcf_record.hpp
vcf_window.hpp
version.hpp	Some stuff that is totally not imporatant, but nice
window.hpp
tree/formats/newick/writer.cpp
tree/formats/phyloxml/writer.cpp	Implementation of functions for reading and writing Phyloxml files
utils/formats/bmp/writer.cpp
utils/formats/json/writer.cpp
utils/formats/nexus/writer.cpp
utils/formats/xml/writer.cpp
tree/formats/newick/writer.hpp
tree/formats/phyloxml/writer.hpp
utils/containers/matrix/writer.hpp
utils/formats/bmp/writer.hpp
utils/formats/json/writer.hpp
utils/formats/nexus/writer.hpp
utils/formats/xml/writer.hpp