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.
TagSelectorA structure to select a tag from a TagList.
Bundle2Stores references to two arbitrary objects.
Bundle3Stores references to three arbitrary objects.
Bundle5Stores references to five arbitrary objects.
PairStores two arbitrary objects.
TripleStores three arbitrary objects.
TupleA plain fixed-length string.
AlignAn alignment of sequences.
AlignColsPseudo columns container for row-based alignment classes.
AlignConfigThe AlignConfig class encapsulates how DP is carried out. It indicates at what ends gaps are free, the so-called free ends-space alignments.
FragmentA type for ungapped, pairwise segment matches.
GapAnchorStores the position of an alignment character in sequence-space and in gap-space.
GapsStores the gaps in a gapped sequences.
AllocatorManager for allocated memory.
HolderManages relationship to another object.
IterIterator that is used to traverse containers.
LexicalComparator for lexical comparison.
ProxyEmulates object of another class.
SimpleTypeImplementation for "simple" types.
ToStdAllocatorEmulates standard conform allocator.
BlastHitObject for storing Blast hits.
BlastHspObject for storing Blast HSPs.
BlastReportObject for storing Blast report information.
Fragment Store
AlignQualityStoreElementStores alignment qualities.
AlignedReadLayoutStores a 2-dimensional visible layout of a multi-read alignment.
AlignedReadStoreElementRepresents an alignment between read and contig.
ContigFileRepresents a file containing contigs.
ContigStoreElementRepresents a single contig.
FragmentStoreMulti-Container to store contigs, reads and a multiple alignment between them.
LibraryStoreElementRepresents a fragment library.
MatePairStoreElementRepresents a mate-pair.
NameStoreCacheStores a mapping from names to ids.
ReadStoreElementRepresents a single read (without sequence).
EdgeStumpThe 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 MapAn external property map.
GraphGeneric graph.
IdManagerId manager that provides unique ids for vertices and edges.
InternalMapAn internal property map using member ids.
InternalPointerMapAn internal property map using pointer to members.
InternalRawMapAn internal property map using raw pointer to members.
HardwiredShapeA structure to define a fixed gapped shape.
IndexContains preprocessing data of a fixed text. Allows fast dictionary look-up and advanced computations.
ShapeStores hash value and shape for an ungapped or gapped q-gram.
AsyncRequestAssociated with an asynchronous I/O request.
AutoSeqFormatAuto-detects and stores a file format.
FileRepresents a file.
FileFormatObject that stores a file format.
MapSet/dictionary container.
MarkovModelGives a suitable representation of a Marcov Chain.
CommandLineOptionStores information for a specific command line option.
CommandLineParserStores multiple CommandLineOption objects and parses the command line arguments for these options.
DequeueA double-ended queue implementation on top of a String.
IntervalAndCargoA simple record type that stores an interval and a cargo value.
IntervalTreeA datastructure that efficiently stores intervals.
IntervalTreeNodeElement of IntervalTree.
LocalAlignmentFinderStores the information necessary for local alignment dynamic programming.
MatrixA simple n-dimensional matrix type.
PointAndCargoSimple record class storing a point (one-value interval) and a cargo.
PriorityTypeStores items in such a way that the item with the highest priority is at the top.
ScoreA scoring scheme.
FunctorComplementFunctor that returns the complement nucleotide to a given nucleotide.
FunctorConvertFunctor that converts a TInValue type to a TOutValue type character.
FunctorLowcaseFunctor that returns the lower case character to a given character.
FunctorUpcaseFunctor that returns the upper case character to a given character.
ModifiedAlphabetModifies value types.
ModifiedIteratorAllows to modify arbitrary iterators by specializing what differs from an origin.
ModifiedStringAllows to modify arbitrary strings by specializing what differs from an origin.
Motif Search
FrequencyDistributionHolds 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.
MotifFinderHolds the algorithm parameter values and the motif instance(s) found by the appropriate motif discovery algorithm.
PseudocountHolds the pseudocounts for each residue of a given sequence alphabet.
PipePipes are pop-passive pipeline modules.
PoolPools are push- and pop-passive pipeline modules.
RngRandom Number Generator
FinderHolds the haystack and a current search context.
PatternHolds the needle and preprocessing data (depends on algorithm).
Seed Handling
MemoryManagerSaves and manages data using IDs.
PropertyMapClass used to save additional data together with a MemoryManager.
SeedDescribes a seed.
SeedSetManages seeds for local chaining and merging algorithms.
ConcatenatorManyToOneA sequence class that virtually concatenates all sequences in a StringSet.
GapsStores the gaps in a gapped sequences.
SegmentA contiguous part of a sequence.
StringGeneral purpose container for sequences.
StringSetA container class for a set of strings.
SeqAn - Sequence Analysis Library -

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