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

TagSelector | A structure to select a tag from a TagList.

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.

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.
Fragment | A type for ungapped, pairwise segment matches.
GapAnchor | Stores the position of an alignment character in sequence-space and in gap-space.
Gaps | Stores the gaps in a gapped sequences.

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.
Proxy | Emulates object of another class.
SimpleType | Implementation for "simple" types.
ToStdAllocator | Emulates standard conform allocator.

Blast

BlastHit | Object for storing Blast hits.
BlastHsp | Object for storing Blast HSPs.
BlastReport | Object for storing Blast report information.

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.
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).

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

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.
Shape | Stores hash value and shape for an ungapped or gapped q-gram.

Input/Output

AsyncRequest | Associated with an asynchronous I/O request.
AutoSeqFormat | Auto-detects and stores a file format.
File | Represents a file.
FileFormat | Object that stores a file format.

Map

Map | Set/dictionary container.

MarkovModel

MarkovModel | Gives a suitable representation of a Marcov Chain.

Miscellaneous

CommandLineOption | Stores information for a specific command line option.
CommandLineParser | Stores multiple CommandLineOption 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.

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.
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

MemoryManager | Saves and manages data using IDs.
PropertyMap | Class used to save additional data together with a MemoryManager.
Seed | Describes a seed.
SeedSet | Manages seeds for local chaining and merging algorithms.

Sequences

ConcatenatorManyToOne | A sequence class that virtually concatenates all sequences in a StringSet.
Gaps | Stores the gaps in a gapped sequences.
Segment | A contiguous part of a sequence.
String | General purpose container for sequences.
StringSet | A container class for a set of strings.

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