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

ArgumentParsre |

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.

BED I/O

BedIOContext | The I/O context to use for BED I/O.
BedRecord | Data structure for storing BED records.
BedRgb | RGB color for Bed12 BedRecord.
BedStream | High-level BED I/O class.

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, multiple read alignments and genome annotations.
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.
GffStream | High-level GFF/GTF I/O class.

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. In combination with a Finder or a VSTree Iterator it 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

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.

Parallelism

Splitter | Splits an interval into subintervals.

Pipelining

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

ROI I/O

RoiIOContext | The I/O context to use for ROI I/O.

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 | A seed in a dotplot.
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.

VCF I/O

VcfHeader | Store VCF Header information.
VcfHeaderRecord | Store key/value pair for VCF header records.
VcfIOContext | The I/O context to use for VCF I/O.
VcfRecord | Information for one VCF record.
VcfStream | High-level VCF I/O class.

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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