▼Ngenesis | Container namespace for all symbols of genesis in order to keep them separate when used as a library |
►Nexcept | |
CException | Base class for genesis exceptions |
CExistingFileError | Exception class that is thrown if trying to write to an existing file |
CGzipError | Exception class thrown by failed gzip/zlib operations |
CIOError | Exception class for general input/output errors |
►Nplacement | |
CEpcaData | Helper stucture that collects the output of epca() |
CJplaceReader | Read Jplace data |
CJplaceWriter | Write Jplace data |
CNodeDistanceHistogram | Simple histogram data structure with equal sized bins |
CNodeDistanceHistogramSet | Collection of NodeDistanceHistograms that describes one Sample |
CPlacementEdgeData | Data class for PlacementTreeEdges. Stores the branch length of the edge, and the edge_num , as defined in the jplace standard |
CPlacementNodeData | Data class for PlacementTreeNodes. Stores a node name |
CPlacementTreeNewickReader | |
CPlacementTreeNewickReaderPlugin | |
CPlacementTreeNewickWriter | |
CPlacementTreeNewickWriterPlugin | |
CPquery | A pquery holds a set of PqueryPlacements and a set of PqueryNames |
CPqueryName | A name of a Pquery and its multiplicity |
CPqueryPlacement | One placement position of a Pquery on a Tree |
CPqueryPlacementPlain | Simple POD struct for a Placement used for speeding up some calculations |
CPqueryPlain | Simple POD struct that stores the information of a Pquery in a simple format for speeding up some calculations |
CSample | Manage a set of Pqueries along with the PlacementTree where the PqueryPlacements are placed on |
CSampleSerializer | |
CSampleSet | Store a set of Samples with associated names |
CSimulator | Simulate Pqueries on the Tree of a Sample |
CSimulatorEdgeDistribution | |
►CSimulatorExtraPlacementDistribution | Generate a certain number of additional PqueryPlacements around a given PlacementTreeEdge |
CEdgeProximity | |
CSimulatorLikeWeightRatioDistribution | |
CSimulatorPendantLengthDistribution | |
CSimulatorProximalLengthDistribution | |
►Npopulation | |
CAfsPileupRecord | Helper to store the data of one pileup line/record needed for the Boitard et al Allele Frequency Estimation computation |
CAlleleFrequencyWindow | |
CBaseCounts | One set of nucleotide base counts, for example for a given sample that represents a pool of sequenced individuals |
CBaseCountsStatus | |
►CBaseWindowIterator | Base iterator class for Windows over the chromosomes of a genome |
CBaseIterator | Internal PIMPL-like implementation of the iterator that produces Windows |
CIterator | Internal public iterator that produces Windows |
►CBedReader | Reader for BED (Browser Extensible Data) files |
CFeature | Store all values that can typically appear in the columns of a BED file |
CEmptyAccumulator | Empty helper data struct to serve as a dummy for Window |
CEmptyGenomeData | Helper struct to define a default empty data for the classes GenomeLocus, GenomeRegion, and GenomeRegionList |
CGenomeHeatmap | |
CGenomeLocus | A single locus, that is, a position (or coordinate) on a chromosome |
CGenomeRegion | A region (between two positions) on a chromosome |
CGenomeRegionList | List of regions in a genome, for each chromosome |
►CGffReader | Reader for GFF2 and GFF3 (General Feature Format) and GTF (General Transfer Format) files |
CFeature | |
►CHeatmapColorization | |
CSpectrum | |
CHeatmapMatrix | Matrix to capture and accumulate columns of per-position or per-window values along a chromosome |
CHtsFile | Wrap an ::htsFile struct |
CPoolDiversityResults | Data struct to collect all diversity statistics computed by pool_diversity_measures() |
CPoolDiversitySettings | Settings used by different pool-sequencing corrected diversity statistics |
►CRegionWindowIterator | Iterator for Windows representing regions of a genome |
CIterator | Internal iterator over the data |
►CSamVariantInputIterator | Input iterator for SAM/BAM/CRAM files that produces a Variant per genome position |
CIterator | Iterator over loci of the input sources |
CSimplePileupInputIterator | Iterate an input source and parse it as a (m)pileup file |
►CSimplePileupReader | Reader for line-by-line assessment of (m)pileup files |
CRecord | Single line/record from a pileup file |
CSample | One sample in a pileup line/record |
►CSlidingIntervalWindowIterator | Iterator for sliding Windows of fixed sized intervals over the chromosomes of a genome |
CDerivedIterator | Internal iterator that produces Windows |
►CSlidingVariantsWindowIterator | Iterator for sliding Windows of fixed sized intervals over the chromosomes of a genome |
CDerivedIterator | Internal iterator that produces Windows |
CSlidingWindowGenerator | Generator for sliding Windows over the chromosomes of a genome |
►CSortedBaseCounts | Ordered array of base counts for the four nucleotides |
CBaseCount | Combination of a nucleotide base and its count |
CSyncInputIterator | Iterate an input source and parse it as a sync file |
CSyncReader | Reader for PoPoolation2's "synchronized" files |
CVariant | A single variant at a position in a chromosome, along with BaseCounts for a set of samples |
CVariantInputIteratorData | Data storage for input-specific information when traversing a variant file |
►CVariantParallelInputIterator | Iterate multiple input sources that yield Variants in parallel |
CIterator | Iterator over loci of the input sources |
CVcfFormatHelper | Provide htslib helper functions |
CVcfFormatIterator | Iterate the FORMAT information for the samples in a SNP/variant line in a VCF/BCF file |
CVcfGenotype | Simple wrapper class for one genotype field for a sample |
CVcfHeader | Capture the information from a header of a VCF/BCF file |
CVcfInputIterator | Iterate an input source and parse it as a VCF/BCF file |
CVcfRecord | Capture the information of a single SNP/variant line in a VCF/BCF file |
CVcfSpecification | Collect the four required keys that describe an INFO or FORMAT sub-field of VCF/BCF files |
►CWindow | Window over the chromosomes of a genome |
CEntry | Data that is stored per entry that was enqueued in a window |
►Nsequence | |
CFastaInputIterator | Iterate an input source and parse it as Fasta sequences |
CFastaOutputIterator | Write Fasta data, sequentially |
CFastaReader | Read Fasta sequence data |
CFastaWriter | Write Fasta data |
CFastqInputIterator | Iterate an input source and parse it as Fastq sequences |
CFastqOutputIterator | Write Fastq data, sequentially |
CFastqReader | Read Fastq sequence data |
CFastqWriter | Write Fastq data |
CLabelAttributes | |
►CPhylipReader | Read Phylip sequence data |
CHeader | Helper that stores the header information of a Phylip file |
CPhylipWriter | |
CPrinterBitmap | Print the sites of a SequenceSet as pixels in a bitmap |
CPrinterSimple | Simple printer class for Sequences and SequenceSets |
CSequence | |
CSequenceSet | Store a set of Sequences |
CSignatureSpecifications | Specifications for calculating signatures (like k-mer counts) from Sequences |
CSiteCounts | Store counts of the occurence for certain characters at the sites of Sequences |
►Ntaxonomy | |
CBaseTaxonData | Base class for storing data on Taxa of a Taxonomy |
CBreadthFirstSearch | Tag used for find_taxon() |
CDepthFirstSearch | Tag used for find_taxon() |
CEntropyTaxonData | |
CIteratorPreorder | |
CNcbiName | |
CNcbiNode | |
CPrinterNested | Simple printer class for Taxonomy |
CPruneByEntropySettings | Store settings for the Taxonomy pruning algorithm prune_by_entropy() |
CTaxon | Store a Taxon, i.e., an element in a Taxonomy, with its name, rank, ID and sub-taxa |
CTaxonomy | Store a Taxonomy, i.e., a nested hierarchy of Taxa |
►CTaxonomyReader | Read Taxonomy file formats |
CLine | Internal helper structure that stores the relevant data of one line while reading |
CTaxonomyWriter | Write a Taxonomy as a list of Taxopaths |
CTaxopath | Helper class to store a taxonomic path |
CTaxopathGenerator | Helper class to generate a taxonomic path string from a Taxopath object or a Taxon |
CTaxopathParser | Helper class to parse a string containing a taxonomic path string into a Taxopath object |
►Ntree | |
CAttributeTreeEdgeData | Data class for AttributeTreeEdges |
CAttributeTreeNodeData | Data class for AttributeTreeNodes |
CBalanceData | Data needed to calculate balances |
CBalanceSettings | Settings to calculate balances and the Phylogenetic ILR Transform |
CBaseEdgeData | Base class for storing data on Edges of a Tree |
CBaseNodeData | Base class for storing data on Nodes of a Tree |
CBipartition | |
CCircularLayout | |
CColorWriterPlugin | Base class for creating plugin classes that allow coloring of Tree edges |
CCommonEdgeData | Common class containing the commonly needed data for tree edges |
CCommonNodeData | Common class containing the commonly needed data for tree nodes |
CCommonTreeNewickReader | Read default Newick trees, i.e., trees with names and branch lengths |
CCommonTreeNewickReaderPlugin | Provide a set of plugin functions for NewickReader to read a CommonTree |
CCommonTreeNewickWriter | Write default Newick trees, i.e., trees with names and branch lengths |
CCommonTreeNewickWriterPlugin | Provide a set of plugin functions for NewickWriter to write a CommonTree |
CCommonTreePhyloxmlWriter | |
CCommonTreePhyloxmlWriterPlugin | |
CHeatTreeParameters | |
CIndexedAttributeTreeNewickReader | Read Newick trees with ordered attributes for the Nodes and Edges |
CIndexedAttributeTreeNewickReaderPlugin | Provide a set of plugin functions for NewickReader to read ordered attributes of the Nodes and Edges into an AttributeTree |
CIteratorEulertour | |
CIteratorLevelorder | |
CIteratorNodeLinks | |
CIteratorPath | |
CIteratorPathSet | Iterate the path between two TreeNodes (non-linearily), given their lowest common ancestor (LCA) |
CIteratorPostorder | |
CIteratorPreorder | |
CKeyedAttributeTreeNewickReader | Read default Newick trees, i.e., trees with names and branch lengths |
CKeyedAttributeTreeNewickReaderPlugin | Provide a set of plugin functions for NewickReader to read key-value-pair data attributes into an AttributeTree |
CLayoutBase | |
CLayoutEdgeData | Data class for LayoutTreeEdges |
CLayoutNodeData | Data class for LayoutTreeNodes |
CLayoutParameters | |
CLcaLookup | Fast lookup of the lowest common ancestor (LCA) of two TreeNodes, relative to an arbitrary root node |
CMassTreeEdgeData | Data class for MassTreeEdges. Stores the branch length and a list of masses with their positions along the edge |
CMassTreeKmeans | |
CMassTreeNodeData | Data class for MassTreeNodes. Stores taxon names |
CNewickBroker | Stores a Newick tree in an intermediate format that can be further processed into a Tree |
CNewickBrokerElement | Store the information for one element of a Newick tree |
CNewickColorWriterPlugin | Plugin class for Newick output that allows coloring of edges |
CNewickInputIterator | Iterate an input stream and parse it as Newick trees |
CNewickReader | |
CNewickWriter | Write a Tree to Newick format |
CPhyloFactor | A single phylogenetic factor |
CPhyloFactorCladeColors | Store a set of colors for making visualizations of the clades of all phylo factors |
CPhyloFactorSingleColors | Store a set of colors for making visualizations of individual phylo factors |
CPhyloxmlColorWriterPlugin | Plugin class for PhyloXML output that allows coloring of edges |
CPhyloxmlWriter | Write a Tree to Phyloxml format |
CPrinterCompact | Print a Tree in a compact form, i.e., each node and edge on one line |
CPrinterDetailed | Print a text representation of the Tree, showing all nodes, edges and links with their indices |
CPrinterTable | Print lists of all nodes, edges and links including their indices and connections with each other |
CRectangularLayout | |
CSimpleNewickEdgeData | Data class for SimpleNewickTreeEdges |
CSimpleNewickNodeData | Data class for SimpleNewickTreeNodes |
CSimpleNewickTreeNewickReader | |
CSimpleNewickTreeNewickReaderPlugin | |
CSimpleNewickTreeNewickWriter | |
CSimpleNewickTreeNewickWriterPlugin | |
►CSquashClustering | Perform Squash Clustering |
CCluster | |
CMerger | |
CSubtree | Reference to a subtree of a Tree |
CTree | Class for representing phylogenetic trees |
CTreeEdge | |
CTreeLink | |
CTreeNode | |
CTreeSet | |
►Nutils | |
CArrowOperatorProxy | Proxy class to hold an element accessible via arrow operator |
CAsynchronousReader | Read bytes from an InputSource into a char buffer |
CBadOptionalAccess | Optional access error for empty values |
CBaseInputSource | Abstract base class for reading byte data from input sources |
CBaseOutputTarget | Abstract base class for writing data to an output target |
CBitvector | |
CBitvectorHash | Helper structure that yields the hash of a given Bitvector |
CBitvectorXhash | Helper structer that yields the x_hash of a given Bitvector |
►CBmpWriter | Write Bitmap image files |
CBitmapFileheader | Bitmap File Header |
CBitmapInfo | Bitmap info that describes dimensions and color information |
CBitmapInfoheader | Bitmap Info Header |
CRgbQuad | Palette entry that describes an RGB Color |
CCharLookup | Simple lookup table providing a value lookup for each ASCII char (0-127) |
CColor | |
CColorMap | Store a list of colors and offer them as a map for values in range [ 0.0, 1.0 ] |
CColorNormalization | Base class for color normalization |
CColorNormalizationBoundary | Color normalization that maps to discrete intervals |
CColorNormalizationDiverging | Color normalization for a diverging scale |
CColorNormalizationLinear | Default Color normalization, using a sequential linear scaling in the range [ min, max ] |
CColorNormalizationLogarithmic | Color normalization for a logarithmic scale |
CCsvInputIterator | |
CCsvReader | Read Comma/Character Separated Values (CSV) data and other delimiter-separated formats |
►CDataframe | |
CColumn | |
CColumnBase | |
CDataframeReader | |
CDereferenceIterator | Iterator class that exposes elements in a container of pointers |
CDeserializer | |
CEmptyIntervalData | Empty class used as default for Interval data |
CEmptyLambdaIteratorData | Empty helper data struct to serve as a dummy for LambdaIterator |
CEuclideanKmeans | |
CFileInputSource | Input source for reading byte data from a file |
CFileOutputTarget | Output target for writing data to a file |
CFilterIterator | Iterator class that allows to filter an underlying iterator by skipping elements that do not satisfy a given predicate |
CFunctionCache | Simple cache, for example for function return values |
CGeoCoordinate | Geographical coordinates in degrees |
CGlmControl | |
CGlmExtras | |
CGlmFactor | |
CGlmFamily | |
CGlmFreedom | Internal helper structure for GLMs to calcualte the residual degrees of freedom |
CGlmLink | |
CGlmOutput | |
CGzipBlockOStream | Output stream that writes blocks of gzip-compressed data to an underlying wrapped stream, using parallel compression |
CGzipBlockOutputTarget | Output target for writing byte data to a gzip-compressed target in blocks of gzip data |
CGzipIFStream | Input file stream that offers on-the-fly gzip-decompression if needed |
CGzipInputSource | Input source for reading byte data from a gzip/zlib-compressed source |
CGzipIStream | Input stream that offers on-the-fly gzip-decompression if needed |
CGzipOFStream | Out file stream that offers on-the-fly gzip-compression |
CGzipOStream | Output stream that offers on-the-fly gzip-compression |
CGzipOutputTarget | Output target for writing byte data to a gzip/zlib-compressed target |
Chas_input_iterator_properties | |
Chas_input_iterator_properties< T, void_t< decltype(++std::declval< T & >()), decltype(*std::declval< T & >()), decltype(std::declval< T & >()==std::declval< T & >())> > | |
Chash | |
Chash< std::tuple< TT... > > | |
CHistogram | Histogram class for accumulating and summarizing data |
CHistogramAccumulator | Histogram helper class that collects data and builds a fitting Histogram |
CInputBuffer | |
CInputStream | Stream interface for reading data from an InputSource, that keeps track of line and column counters |
CInterval | Type to store an interval (range) between two numbers, as used in the IntervalTree |
CIntervalClosed | Helper type to define a closed [] Interval |
CIntervalLeftOpen | Helper type to define a left open (] Interval |
CIntervalOpen | Helper type to define an open () Interval |
CIntervalRightOpen | Helper type to define a right open [) Interval |
CIntervalTree | Interval tree that enables storing and querying intervals, each containing some data |
CIntervalTreeIterator | Iterate the Intervals stored in an IntervalTree |
CIntervalTreeNode | Node in an IntervalTree |
Cis_bidirectional_iterator_tag_based | Return whether a type is at least a bidirectional iterator |
Cis_bidirectional_iterator_tag_based< T, typename std::enable_if< std::is_base_of< std::bidirectional_iterator_tag, typename std::iterator_traits< T >::iterator_category >::value >::type > | Return whether a type is at least a bidirectional iterator |
Cis_forward_iterator_tag_based | Return whether a type is at least a forward iterator |
Cis_forward_iterator_tag_based< T, typename std::enable_if< std::is_base_of< std::forward_iterator_tag, typename std::iterator_traits< T >::iterator_category >::value >::type > | Return whether a type is at least a forward iterator |
Cis_input_iterator_tag_based | Return whether a type is an at least input iterator |
Cis_input_iterator_tag_based< T, typename std::enable_if< std::is_base_of< std::input_iterator_tag, typename std::iterator_traits< T >::iterator_category >::value >::type > | Return whether a type is an at least input iterator |
Cis_iterator_tag_based | Return whether a type is an iterator |
Cis_iterator_tag_based< T, typename std::enable_if< std::is_base_of< std::input_iterator_tag, typename std::iterator_traits< T >::iterator_category >::value||std::is_same< std::output_iterator_tag, typename std::iterator_traits< T >::iterator_category >::value >::type > | Return whether a type is an iterator |
Cis_output_iterator_tag_based | Return whether a type is an at least output iterator |
Cis_output_iterator_tag_based< T, typename std::enable_if< std::is_base_of< std::output_iterator_tag, typename std::iterator_traits< T >::iterator_category >::value >::type > | Return whether a type is an at least output iterator |
Cis_random_access_iterator_tag_based | Return whether a type is at least a random access iterator |
Cis_random_access_iterator_tag_based< T, typename std::enable_if< std::is_base_of< std::random_access_iterator_tag, typename std::iterator_traits< T >::iterator_category >::value >::type > | Return whether a type is at least a random access iterator |
CIteratorDeletions | Take a TwobitVector sequence and iterate over all possible deletions of its values |
CIteratorInsertions | |
CIteratorSubstitutions | |
CJsonDocument | Store a Json value of any kind |
►CJsonIterator | Template for a random access iterator for the JsonDocument class |
CInternalIterator | Iterator value |
CPrimitiveIterator | Iterator for primitive JSON types |
CJsonReader | Read Json data into a JsonDocument |
CJsonWriter | Write Json data from a JsonDocument |
CKmeans | |
CKmeansClusteringInfo | Helper POD that stores the variances and number of data points of each centroid, as well as the distances from all data points to their assigned centroids |
►CLambdaIterator | Type erasure for iterators, using std::function to eliminate the underlying input type |
CIterator | Internal iterator over the data |
CLinearFunction | Data structer to keep the two parameters of a linear function: its slope, and its intercept |
CLogging | Logging class with easy and fast usage |
CLoggingDetails | POD stuct containing the settings for which information is included with each logging message |
CLoggingScopeLevel | Class that sets the Logging Level to a value von construction and set it back on destruction. This is used by the log scope level macro |
CMatrix | |
►CMatrixCol | View into a Matrix column |
CIterator | Random access iterator into a Matrix column |
CMatrixReader | |
►CMatrixRow | View into a Matrix row |
CIterator | Random access iterator into a Matrix row |
CMatrixWriter | |
CMD5 | Calculate MD5 hashes for strings and files |
CMeanStddevPair | Store a mean and a standard deviation value |
CMinMaxPair | Store a pair of min and max values |
CMruCache | Most Recently Used Cache |
CNaturalLess | Functor class to compare to strings with natural "human" sorting, see compare_natural() |
CNexusBlock | |
CNexusDocument | |
CNexusTaxa | |
►CNexusTrees | |
CEntry | |
CNexusWriter | |
►Cnullopt_t | Type for nullopt |
Cinit | |
COptional | Simplistic optional: requires T to be default constructible, copyable |
COptions | Simple Options class for application-wide configuration and settings |
CPcaData | Helper stucture that collects the output of principal_component_analysis() |
CQuartiles | Store the values of quartiles: q0 == min , q1 == 25% , q2 == 50% , q3 == 75% , q4 == max |
CRange | Simple wrapper for typical begin() and end() iterators, to be used in range-based for loops |
CRangeMinimumQuery | Class that allows to efficiently find the index of the minimum element within an interval of an array of integer values |
CSerializer | |
CSHA1 | Calculate SHA1 hashes for strings and files |
CSHA256 | Calculate SHA256 hashes for strings and files |
CStreamInputSource | Input source for reading byte data from an istream |
CStreamOutputTarget | Output target for writing data to a stream |
CStrictFStream | Stream that defines a strict wrapper around std::fstream |
CStrictFStreamHolder | Helper class template for managing the construction order between stream classes |
CStrictIFStream | Stream that defines a strict wrapper around std::ifstream |
CStrictOFStream | Stream that defines a strict wrapper around std::ofstream |
CStringInputSource | Input source for reading byte data from a string |
CStringOutputTarget | Output target for writing data to a string |
CStyle | Simple text style class for colorized and bold output to a terminal |
CSvgBox | |
CSvgCircle | |
CSvgColorBarSettings | |
CSvgDefinitions | |
CSvgDocument | |
CSvgDrawingOptions | |
CSvgEllipse | |
CSvgFill | |
CSvgFont | |
CSvgGradientLinear | |
CSvgGradientStop | |
CSvgGroup | |
CSvgImage | |
CSvgLine | |
CSvgMargin | |
CSvgMatrixSettings | |
CSvgObject | |
CSvgPath | |
CSvgPoint | |
CSvgPolygon | |
CSvgPolyline | |
CSvgRect | |
CSvgSize | |
CSvgStroke | |
CSvgText | |
►CSvgTransform | |
CMatrix | |
CRotate | |
CScale | |
CSkew | |
CTransformation | Internal helper class used as an abstraction to be able to store Transformations without need for inheritance and virtual functions within the different transformation types |
CTranslate | |
CSvgUse | |
CSynchronousReader | Read bytes from an InputSource into a char buffer |
►CTable | |
CColumn | |
►CTableLayout | |
CBinder | Helper struct to bind a layout to a table |
CLine | One line of the TableLayout |
CThreadPool | Thread pool for distributed work |
►CTickmarks | Helper class to find "nice" tickmark intervals for creating scales and axes |
CLabeledTick | |
CTransformIterator | Iterator class that allows to transform an underlying iterator by applying a function to each element before dereferencing |
CTridiagonalDecompositionData | Helper structure used for the eigenvalue decomposition in reduce_to_tridiagonal_matrix() and tridiagonal_ql_algorithm(). See there for details |
CTwobitVector | |
CXmlComment | |
CXmlDocument | |
CXmlElement | |
CXmlMarkup | |
CXmlValue | |
CXmlWriter | Write Xml data |
▼Nstd | STL namespace |
Chash< genesis::taxonomy::Taxopath > | Hash function for Taxopath |
Chash< genesis::utils::Bitvector > | Specialization of std::hash for the Bitvector class |
Chash< genesis::utils::MD5::DigestType > | Hash function for MD5 digestes |
Chash< genesis::utils::SHA1::DigestType > | Hash function for SHA1 digestes |
Chash< genesis::utils::SHA256::DigestType > | Hash function for SHA256 digestes |