Classes
This section lists the main classes provided by SeqAn.
Many of these classes are templates that can be specialized using Template Subclassing.
See the section Specializations for a list of these specializations.
Classes
Aggregates
| Stores references to two arbitrary objects. | |
| Stores references to three arbitrary objects. | |
| Stores references to five arbitrary objects. | |
| Stores two arbitrary objects. | |
| Stores three arbitrary objects. | |
| A plain fixed-length string. |
Alignment Free
| Used to specify parameters and methods for alignment-free sequence comparison |
Alignments
| An alignment of sequences. | |
| Pseudo columns container for row-based alignment classes. | |
| The AlignConfig class encapsulates how DP is carried out. It indicates at what ends gaps are free, the so-called free ends-space alignments. | |
| Wrapper for a pointer to a sequence and a position in this sequence. | |
| A type for ungapped, pairwise segment matches. | |
| Stores the position of an alignment character in sequence-space and in gap-space. | |
| Efficient storage of gaps for a sequence. | |
| Enumerate local alignments using the Waterman-Eggert algorithm. |
Alphabets
| Alphabet type for profiles over another alphabet. |
BAM I/O
| Represent a record from a BAM/SAM file. | |
| Stores the information of the BAM header. | |
| Represents a header entry in a SAM file or the header section of the BAM header. | |
| The I/O context to use for BAM I/O. | |
| Access to BAM Indices. | |
| Class that provides an easy to use interface for reading and writing SAM and BAM files. | |
| Indexes start positions of BAM tags in a CharString and provides a dict-like API. | |
| Represent a record from a Gff file. |
BED I/O
| The I/O context to use for BED I/O. | |
| Data structure for storing BED records. | |
| RGB color for Bed12 BedRecord. | |
| High-level BED I/O class. |
Basic
| Manager for allocated memory. | |
| Manages relationship to another object. | |
| Iterator that is used to traverse containers. | |
| Comparator for lexical comparison. | |
| Value type for computation in log-space. | |
| Emulates object of another class. | |
| Implementation for "simple" types. | |
| A structure to select a tag from a TagList. | |
| Emulates standard conform allocator. | |
| Helper data structure for handling volatile data. |
File
| A structure to memory-map a file. |
Fragment Store
| Stores alignment qualities. | |
| Stores a 2-dimensional visible layout of a multi-read alignment. | |
| Represents an alignment between read and contig. | |
| Represents an annotation of a contig feature. | |
| Indexes start positions of BAM tags in a CharString and provides a dict-like API. | |
| One entry of a CIGAR string. | |
| Represents a file containing contigs. | |
| Represents a single contig. | |
| Multi container to store contigs, reads, multiple read alignments and genome annotations. | |
| Represents a fragment library. | |
| Represents a mate-pair. | |
| Stores a mapping from names to ids. | |
| Represents a single read (without sequence). |
GFF I/O
| The I/O context to use for GFF I/O. | |
| High-level GFF/GTF I/O class. |
Graph
| The EdgeStump class encapsulates a single edge. It represents either a list node in the adjacency list of a graph or an array field if edges are stored in an array. | |
| An external property map. | |
| Generic graph. | |
| Id manager that provides unique ids for vertices and edges. | |
| An internal property map using member ids. | |
| An internal property map using pointer to members. | |
| An internal property map using raw pointer to members. |
Index
| A suffix array storing only a few suffix array entries and computing the remaining on demand. | |
| A structure to define a fixed gapped shape. | |
| Contains preprocessing data of a fixed text. In combination with a Finder or a VSTree Iterator it allows fast dictionary look-up and advanced computations. | |
| LfTable is an object storing all necessary information for the LF-mapping. | |
| The prefix-sum table is a data structure which stores for each character the number of smaller lexicographic smaller characters in a given text. | |
| A rank dictionary is a data structure to store the rank of an element of a sequence at every position of the sequence. | |
| A bit string supporting rank queries in constant time. | |
| Store information about a repeat. | |
| A rank dictionary, additional storing sentinel character which are not accounted for in a rank querry. | |
| Stores hash value and shape for an ungapped or gapped q-gram. | |
| A string storing only a fraction of the values of the original string.. |
Input/Output
| Associated with an asynchronous I/O request. | |
| Auto-detects and stores a file format. | |
| Data type for storing FAI indices. | |
| Represents a file. | |
| Object that stores a file format. | |
| Store information about a genomic region. | |
| manipulates a RecordReader -Object so that it operates only on one buffer | |
| Buffer management for streams. | |
| Configuration for writing sequence (FASTA/FASTQ) files. | |
| High-level reading and writing of sequences. | |
| Abstract base class to fulfill the StreamConcept concept. |
Local Match Store
| Stores information about local matches. | |
| Stores information about local matches. | |
| Stores information about local matches. |
Map
| Set/dictionary container. |
MarkovModel
| Gives a suitable representation of a Marcov Chain. |
Miscellaneous
| Accumulator base class. | |
| Stores information for a specific command line argument. It can be either an argument of a ArgParseArgument or directly an Argument on the command line. | |
| Stores information for a specific command line option. | |
| Stores multiple ArgParseOption objects and parses the command line arguments for these options. | |
| A double-ended queue implementation on top of a String. | |
| A simple record type that stores an interval and a cargo value. | |
| A datastructure that efficiently stores intervals. | |
| Element of IntervalTree. | |
| Stores the information necessary for local alignment dynamic programming. | |
| A simple n-dimensional matrix type. | |
| Simple record class storing a point (one-value interval) and a cargo. | |
| Stores items in such a way that the item with the highest priority is at the top. | |
| A scoring scheme. | |
| Class to enumerate all strings within a given edit/Hamming distance. | |
| Container for string documentation on a command line tool. | |
| Union-Find data structure. |
Modifier
| Functor that returns the complement nucleotide to a given nucleotide. | |
| Functor that converts a | |
| Functor that returns the lower case character to a given character. | |
| Functor that returns the upper case character to a given character. | |
| Modifies value types. | |
| Allows to modify arbitrary iterators by specializing what differs from an origin. | |
| Allows to modify arbitrary strings by specializing what differs from an origin. |
Motif Search
| Holds a collection of objects of a specific type, where each object represents the frequency (absolute or relative probability) of a particular residue which is a member of a fixed sequence alphabet. | |
| Holds the algorithm parameter values and the motif instance(s) found by the appropriate motif discovery algorithm. | |
| Holds the algorithm parameter values and the motif instance(s) found by the appropriate motif discovery algorithm. | |
| Holds the pseudocounts for each residue of a given sequence alphabet. |
Parallelism
| Splits an interval into subintervals. |
Pipelining
| Pipes are pop-passive pipeline modules. | |
| Pools are push- and pop-passive pipeline modules. |
ROI I/O
| The I/O context to use for ROI I/O. |
Searching
| Holds the haystack and a current search context. | |
| Holds the needle and preprocessing data (depends on algorithm). |
Seed Handling
| A seed in a dotplot. | |
| Store the information about a seed segment. | |
| Handles a set of seeds with local chaining on adding seeds. |
Sequences
| A sequence class that virtually concatenates all sequences in a StringSet. | |
| Specifies the strategy and all necessary parameters used to journal a sequence to a reference sequence. | |
| A contiguous part of a sequence. | |
| A sequence container with generic alphabet and many specializations. | |
| A container class for a set of strings. |
VCF I/O
| Store VCF Header information. | |
| Store key/value pair for VCF header records. | |
| The I/O context to use for VCF I/O. | |
| Information for one VCF record. | |
| High-level VCF I/O class. |
WaveletTree
| A special format to encode the structure of a wavelet tree. The structure is very space efficient because only one position is stored which encodes where the left and right subtree of a given node exist. |
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