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.
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.
Alignment Free
AFScoreUsed to specify parameters and methods for alignment-free sequence comparison
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.
ConsensusScoreSequenceEntryWrapper for a pointer to a sequence and a position in this sequence.
FragmentA type for ungapped, pairwise segment matches.
GapAnchorStores the position of an alignment character in sequence-space and in gap-space.
GapsEfficient storage of gaps for a sequence.
LocalAlignmentEnumeratorEnumerate local alignments using the Waterman-Eggert algorithm.
ProfileCharAlphabet type for profiles over another alphabet.
BamAlignmentRecordRepresent a record from a BAM/SAM file.
BamHeaderStores the information of the BAM header.
BamHeaderRecordRepresents a header entry in a SAM file or the header section of the BAM header.
BamIOContextThe I/O context to use for BAM I/O.
BamIndexAccess to BAM Indices.
BamStreamClass that provides an easy to use interface for reading and writing SAM and BAM files.
BamTagsDictIndexes start positions of BAM tags in a CharString and provides a dict-like API.
GffRecordRepresent a record from a Gff file.
BedIOContextThe I/O context to use for BED I/O.
BedRecordData structure for storing BED records.
BedRgbRGB color for Bed12 BedRecord.
BedStreamHigh-level BED I/O class.
AllocatorManager for allocated memory.
HolderManages relationship to another object.
IterIterator that is used to traverse containers.
LexicalComparator for lexical comparison.
LogProbValue type for computation in log-space.
ProxyEmulates object of another class.
SimpleTypeImplementation for "simple" types.
TagSelectorA structure to select a tag from a TagList.
ToStdAllocatorEmulates standard conform allocator.
VolatilePtrHelper data structure for handling volatile data.
FileMappingA structure to memory-map a file.
Fragment Store
AlignQualityStoreElementStores alignment qualities.
AlignedReadLayoutStores a 2-dimensional visible layout of a multi-read alignment.
AlignedReadStoreElementRepresents an alignment between read and contig.
AnnotationStoreElementRepresents an annotation of a contig feature.
BamTagsDictIndexes start positions of BAM tags in a CharString and provides a dict-like API.
CigarElementOne entry of a CIGAR string.
ContigFileRepresents a file containing contigs.
ContigStoreElementRepresents a single contig.
FragmentStoreMulti container to store contigs, reads, multiple read alignments and genome annotations.
LibraryStoreElementRepresents a fragment library.
MatePairStoreElementRepresents a mate-pair.
NameStoreCacheStores a mapping from names to ids.
ReadStoreElementRepresents a single read (without sequence).
GffIOContextThe I/O context to use for GFF I/O.
GffStreamHigh-level GFF/GTF I/O class.
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.
CompressedSAA suffix array storing only a few suffix array entries and computing the remaining on demand.
HardwiredShapeA structure to define a fixed gapped shape.
IndexContains preprocessing data of a fixed text. In combination with a Finder or a VSTree Iterator it allows fast dictionary look-up and advanced computations.
LfTableLfTable is an object storing all necessary information for the LF-mapping.
PrefixSumTableThe prefix-sum table is a data structure which stores for each character the number of smaller lexicographic smaller characters in a given text.
RankDictionaryA rank dictionary is a data structure to store the rank of an element of a sequence at every position of the sequence.
RankSupportBitStringA bit string supporting rank queries in constant time.
RepeatStore information about a repeat.
SentinelRankDictionaryA rank dictionary, additional storing sentinel character which are not accounted for in a rank querry.
ShapeStores hash value and shape for an ungapped or gapped q-gram.
SparseStringA string storing only a fraction of the values of the original string..
AsyncRequestAssociated with an asynchronous I/O request.
AutoSeqFormatAuto-detects and stores a file format.
FaiIndexData type for storing FAI indices.
FileRepresents a file.
FileFormatObject that stores a file format.
GenomicRegionStore information about a genomic region.
LimitRecordReaderInScopemanipulates a RecordReader -Object so that it operates only on one buffer
RecordReaderBuffer management for streams.
SequenceOutputOptionsConfiguration for writing sequence (FASTA/FASTQ) files.
SequenceStreamHigh-level reading and writing of sequences.
StreamAbstract base class to fulfill the StreamConcept concept.
Local Match Store
LocalMatchStores information about local matches.
LocalMatchStoreStores information about local matches.
LocalMatchStoreConfigStores information about local matches.
MapSet/dictionary container.
MarkovModelGives a suitable representation of a Marcov Chain.
AccumulatorAccumulator base class.
ArgParseArgumentStores information for a specific command line argument. It can be either an argument of a ArgParseArgument or directly an Argument on the command line.
ArgParseOptionStores information for a specific command line option.
ArgumentParserStores multiple ArgParseOption 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.
StringEnumeratorClass to enumerate all strings within a given edit/Hamming distance.
ToolDocContainer for string documentation on a command line tool.
UnionFindUnion-Find data structure.
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.
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.
SplitterSplits an interval into subintervals.
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
SeedA seed in a dotplot.
SeedDiagonalStore the information about a seed segment.
SeedSetHandles a set of seeds with local chaining on adding seeds.
ConcatenatorManyToOneA sequence class that virtually concatenates all sequences in a StringSet.
JoinConfigSpecifies the strategy and all necessary parameters used to journal a sequence to a reference sequence.
SegmentA contiguous part of a sequence.
StringA sequence container with generic alphabet and many specializations.
StringSetA container class for a set of strings.
VcfHeaderStore VCF Header information.
VcfHeaderRecordStore key/value pair for VCF header records.
VcfIOContextThe I/O context to use for VCF I/O.
VcfRecordInformation for one VCF record.
VcfStreamHigh-level VCF I/O class.
RightArrayBinaryTreeA 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.
SeqAn - Sequence Analysis Library -

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