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.

Aggregates

Bundle2	Stores references to two arbitrary objects.
Bundle3	Stores references to three arbitrary objects.
Bundle5	Stores references to five arbitrary objects.
Pair	Stores two arbitrary objects.
Triple	Stores three arbitrary objects.
Tuple	A plain fixed-length string.

Alignment Free

AFScore

Used to specify parameters and methods for alignment-free sequence comparison

Alignments

Align	An alignment of sequences.
AlignCols	Pseudo columns container for row-based alignment classes.
AlignConfig	The AlignConfig class encapsulates how DP is carried out. It indicates at what ends gaps are free, the so-called free ends-space alignments.
ConsensusScoreSequenceEntry	Wrapper for a pointer to a sequence and a position in this sequence.
Fragment	A type for ungapped, pairwise segment matches.
GapAnchor	Stores the position of an alignment character in sequence-space and in gap-space.
Gaps	Efficient storage of gaps for a sequence.
LocalAlignmentEnumerator	Enumerate local alignments using the Waterman-Eggert algorithm.

Alphabets

ProfileChar

Alphabet type for profiles over another alphabet.

BAM I/O

BamAlignmentRecord	Represent a record from a BAM/SAM file.
BamHeader	Stores the information of the BAM header.
BamHeaderRecord	Represents a header entry in a SAM file or the header section of the BAM header.
BamIOContext	The I/O context to use for BAM I/O.
BamIndex	Access to BAM Indices.
BamStream	Class that provides an easy to use interface for reading and writing SAM and BAM files.
BamTagsDict	Indexes start positions of BAM tags in a CharString and provides a dict-like API.
GffRecord	Represent a record from a Gff file.

Basic

Allocator	Manager for allocated memory.
Holder	Manages relationship to another object.
Iter	Iterator that is used to traverse containers.
Lexical	Comparator for lexical comparison.
LogProb	Value type for computation in log-space.
Proxy	Emulates object of another class.
SimpleType	Implementation for "simple" types.
TagSelector	A structure to select a tag from a TagList.
ToStdAllocator	Emulates standard conform allocator.
VolatilePtr	Helper data structure for handling volatile data.

File

FileMapping

A structure to memory-map a file.

Fragment Store

AlignQualityStoreElement	Stores alignment qualities.
AlignedReadLayout	Stores a 2-dimensional visible layout of a multi-read alignment.
AlignedReadStoreElement	Represents an alignment between read and contig.
AnnotationStoreElement	Represents an annotation of a contig feature.
BamTagsDict	Indexes start positions of BAM tags in a CharString and provides a dict-like API.
CigarElement	One entry of a CIGAR string.
ContigFile	Represents a file containing contigs.
ContigStoreElement	Represents a single contig.
FragmentStore	Multi-Container to store contigs, reads and a multiple alignment between them.
LibraryStoreElement	Represents a fragment library.
MatePairStoreElement	Represents a mate-pair.
NameStoreCache	Stores a mapping from names to ids.
ReadStoreElement	Represents a single read (without sequence).

GFF I/O

GffIOContext

The I/O context to use for GFF I/O.

Graph

EdgeStump	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.
External Property Map	An external property map.
Graph	Generic graph.
IdManager	Id manager that provides unique ids for vertices and edges.
InternalMap	An internal property map using member ids.
InternalPointerMap	An internal property map using pointer to members.
InternalRawMap	An internal property map using raw pointer to members.

Index

CompressedSA	A suffix array storing only a few suffix array entries and computing the remaining on demand.
HardwiredShape	A structure to define a fixed gapped shape.
Index	Contains preprocessing data of a fixed text. Allows fast dictionary look-up and advanced computations.
LfTable	LfTable is an object storing all necessary information for the LF-mapping.
PrefixSumTable	The prefix-sum table is a data structure which stores for each character the number of smaller lexicographic smaller characters in a given text.
RankDictionary	A rank dictionary is a data structure to store the rank of an element of a sequence at every position of the sequence.
RankSupportBitString	A bit string supporting rank queries in constant time.
Repeat	Store information about a repeat.
SentinelRankDictionary	A rank dictionary, additional storing sentinel character which are not accounted for in a rank querry.
Shape	Stores hash value and shape for an ungapped or gapped q-gram.
SparseString	A string storing only a fraction of the values of the original string..

Input/Output

AsyncRequest	Associated with an asynchronous I/O request.
AutoSeqFormat	Auto-detects and stores a file format.
FaiIndex	Data type for storing FAI indices.
File	Represents a file.
FileFormat	Object that stores a file format.
GenomicRegion	Store information about a genomic region.
LimitRecordReaderInScope	manipulates a RecordReader -Object so that it operates only on one buffer
RecordReader	Buffer management for streams.
SequenceOutputOptions	Configuration for writing sequence (FASTA/FASTQ) files.
SequenceStream	High-level reading and writing of sequences.
Stream	Abstract base class to fulfill the StreamConcept concept.

Local Match Store

LocalMatch	Stores information about local matches.
LocalMatchStore	Stores information about local matches.
LocalMatchStoreConfig	Stores information about local matches.

Map

Map	Set/dictionary container.

MarkovModel

Gives a suitable representation of a Marcov Chain.

Miscellaneous

Accumulator	Accumulator base class.
ArgParseArgument	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.
ArgParseOption	Stores information for a specific command line option.
ArgumentParser	Stores multiple ArgParseOption objects and parses the command line arguments for these options.
Dequeue	A double-ended queue implementation on top of a String.
IntervalAndCargo	A simple record type that stores an interval and a cargo value.
IntervalTree	A datastructure that efficiently stores intervals.
IntervalTreeNode	Element of IntervalTree.
LocalAlignmentFinder	Stores the information necessary for local alignment dynamic programming.
Matrix	A simple n-dimensional matrix type.
PointAndCargo	Simple record class storing a point (one-value interval) and a cargo.
PriorityType	Stores items in such a way that the item with the highest priority is at the top.
Score	A scoring scheme.
StringEnumerator	Class to enumerate all strings within a given edit/Hamming distance.
ToolDoc	Container for string documentation on a command line tool.
UnionFind	Union-Find data structure.

Modifier

FunctorComplement	Functor that returns the complement nucleotide to a given nucleotide.
FunctorConvert	Functor that converts a TInValue type to a TOutValue type character.
FunctorLowcase	Functor that returns the lower case character to a given character.
FunctorUpcase	Functor that returns the upper case character to a given character.
ModifiedAlphabet	Modifies value types.
ModifiedIterator	Allows to modify arbitrary iterators by specializing what differs from an origin.
ModifiedString	Allows to modify arbitrary strings by specializing what differs from an origin.

Motif Search

FrequencyDistribution	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.
MotifFinder	Holds the algorithm parameter values and the motif instance(s) found by the appropriate motif discovery algorithm.
MotifFinder	Holds the algorithm parameter values and the motif instance(s) found by the appropriate motif discovery algorithm.
Pseudocount	Holds the pseudocounts for each residue of a given sequence alphabet.

Pipelining

Pipe	Pipes are pop-passive pipeline modules.
Pool	Pools are push- and pop-passive pipeline modules.

Random

Pdf	ProbabilityDensityFunction
Rng	Random Number Generator

Searching

Finder	Holds the haystack and a current search context.
Pattern	Holds the needle and preprocessing data (depends on algorithm).

Seed Handling

Seed	Describe a seed.
SeedDiagonal	Store the information about a seed segment.
SeedSet	Handles a set of seeds with local chaining on adding seeds.

Sequences

ConcatenatorManyToOne	A sequence class that virtually concatenates all sequences in a StringSet.
JoinConfig	Specifies the strategy and all necessary parameters used to journal a sequence to a reference sequence.
Segment	A contiguous part of a sequence.
String	A sequence container with generic alphabet and many specializations.
StringSet	A container class for a set of strings.

WaveletTree

RightArrayBinaryTree

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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