Specializations

Specializations refine Class templates using Template Subclassing.

Aggregates

Bit Packed Pair	Stores two arbitrary objects. Saves memory by packing bits with bit fields.
Bit Packed Tuple	A plain fixed-length string. Saves memory by packing bits.
Packed Pair	Stores two arbitrary objects. Saves memory by disabling memory alignment.
Packed Triple	Stores three arbitrary objects. Saves memory by disabling memory alignment.

Alignment Free

D2 AFScore	D2 computes the inner product of the kmer count vectors
D2Star AFScore	D2Star computes the inner product of the standardised kmer count vectors
D2z AFScore	D2z computes a z-score of the inner product of kmer count vectors
N2 AFScore	N2 computes the inner product of the standardised neighbourhood kmer count vectors

Alignments

AnchorGaps	Stores gaps anchors of the first characters behind gaps.
ArrayGaps	Stores length of gap- and non-gapped runs in an array.
Banded LocalAlignmentEnumerator	Banded enumeration of local alignments using the Waterman-Eggert algorithm.
ExactFragment	A type for ungapped, pairwise segment matches.
ExactReversableFragment	A type for ungapped, pairwise segment matches that may be in reverse orientation.
Unbanded LocalAlignmentEnumerator	Unbanded enumeration of local alignments using the Waterman-Eggert algorithm.

Allocators

Chunk Pool Allocator	Allocator that pools one or more consecutive memory blocks of a specific size.
Multi Pool Allocator	Allocator that pools memory blocks.
Simple Allocator	General purpose allocator.
Single Pool Allocator	Allocator that pools memory blocks of specific size.

Alphabets

AminoAcid	Iupac code for amino acids.
Dna	Alphabet for DNA.
Dna5	Alphabet for DNA including 'N' character.
Dna5Q	Alphabet for DNA plus PHRED quality including 'N' character.
DnaQ	Alphabet for DNA plus PHRED quality.
Finite	A finite alphabet of a fixed size.
Iupac	Iupac code for DNA.
Rna	Alphabet for RNA.
Rna5	Alphabet for RNA including 'N' character.
TraceBack	Trace back values.

BAM I/O

BAI BamIndex

Access to BAI (samtools-style) Indices.

BED I/O

Bed12 BedRecord	BedRecord with 12 fields.
Bed3 BedRecord	BedRecord with 3 fields.
Bed4 BedRecord	BedRecord with 4 fields.
Bed5 BedRecord	BedRecord with 5 fields.
Bed6 BedRecord	BedRecord with 6 fields.

Files

Async	File structure supporting synchronous and asynchronous input/output access.
File Reader String	Read sequence data from file.
Sync	File structure supporting synchronous input/output access.

FragmentStore

AnnotationTree Iterator

Iterator of the annotation tree represented by a FragmentStore.

Graph

Adjacency Iterator	Adjacency iterator for Graph.
Alignment Graph	An alignment graph.
Automaton	An Automaton has directed edges, labeled with input symbols, and a distinct start state, called root. The input symbols require the use of a third parameter: The alphabet of the input symbols.
Bfs Iterator	Breath-first search iterator for Graph.
Counting IdManager	Id Manager that just counts the number of ids in use.
Dfs Preorder Iterator	Depth-first search iterator for Graph.
Directed Graph	A directed graph that stores the edges in an adjacency list.
Edge Iterator	Edge iterator for Graph.
Hmm	An Hmm is a directed graph with edges labeled with transition probabilities and emission profiles for each vertex. Vertices correspond to states in an HMM.
Oracle	A factor oracle.
Out-Edge Iterator	Out-edge iterator for Graph.
Tree	A Tree has a distinct root and directed edges. The source vertex of each edge is the parent vertex, the target vertex of each edge is the child. Trees provide fast access to child vertices and the parent.
Trie	A keyword trie.
Undirected Graph	An undirected graph that stores the edges in an adjacency list.
Vertex Iterator	Vertex iterator for Graph.
Word Graph	A special automaton that stores words instead of single characters along its edges.

Holders

Simple Holder	Simple copying wrapper without any additional state.
Tristate Holder	Holder that can be empty, dependent, or owner.

Index

BottomUp Iterator	Iterator for an efficient postorder depth-first search in a suffix tree.
BucketRefinement	An index based on a refined array of sorted q-grams.
FMIndex	An index based on the Burrows-Wheeler transform.
GappedShape	A fixed gapped shape.
GenericShape	A variable gapped shape.
IndexDfi	The Deferred Frequency Index (see Weese and Schulz, "Efficient string mining under constraints via the deferred frequency index").
IndexEsa	The enhanced suffix array index is very fast index, requiring more memory than other indices. In addition to the suffix array an lcp (longest common prefix) table and a child table (containing structural information of the suffix tree) are provided.
IndexQGram	An index based on an array of sorted q-grams. Especially useful for q-gram/k-mer searches.
IndexSa	An index based on a suffix array.
IndexWotd	This index represents a lazy suffix tree, meaning that a path from the tree of the index in only computed, if it is traversed. For details see Giegerich et al., "Efficient implementation of lazy suffix trees".
MaxRepeats Iterator	Iterator to search for all maximal repeats.
MultiMems Iterator	Iterator to search for MultiMems.
Mums Iterator	Iterator to search for all maximum unique matches.
OneGappedShape	A variable shape with one optional gap.
OpenAddressing	An index based on an array of sorted q-grams.
Pizza & Chili Index	An adapter for the Pizza & Chili index API.
SequenceBitMask	The string set bit string dictionary is a string set of rank support bit strings for constant time acces of the rank of a specified character at a specified position.
SequenceBitMask Fibres	Tag to select a specific fibre of a SequenceBitMask.
SimpleShape	A variable length ungapped shape (also called q-gram or k-mer).
SuperMaxRepeats Iterator	Iterator to search for all supermaximal repeats.
SuperMaxRepeatsFast Iterator	Iterator to search for all supermaximal repeats (for enh. suffix arrays only).
TopDown Iterator	Iterator for virtual trees that can go down and right beginning from the root.
TopDownHistory Iterator	String tree iterator that can go down, right, and up. Supports depth-first search.
UngappedShape	A fixed length ungapped shape (also called q-gram or k-mer).
VSTree Iterator	Abstract iterator for suffix trees.
WaveletTree	A wavelet tree is a tree like binary encoding of a text.

Input/Output

BGZF Stream	Reading and writing of BGZF data.
BZ2 File Stream	Wrapper for BZFILE * streams from bzlib.
Char Array Stream	Thin wrapper around char * to the Stream concept.
Double-Pass RecordReader	Record reader specialization for double-pass reading.
Double-Pass String RecordReader	Record reader specialization for double-pass reading
GZ File Stream	Adaption from gzFile of <zlib.h> to streams.
Single-Pass RecordReader	Record reader specialization for single-pass reading.
Single-Pass String RecordReader	Record reader specialization for single-pass reading from memory mapped files.

Iter

RightArrayBinaryTree Iterator

An iterator for RightArrayBinaryTree.

Iterators

Adaptor Iterator	Adapts iterators to RootedIteratorConcept.
AlignColIterator	Iterator for AlignCols pseudo container.
Position Iterator	Adapts Position Iterator to Rooted Iterator.
STD Adaptor Iterator	Adapt STL iterators to SeqAn iterators.

Map

Skiplist	General purpose map container.
VectorSet	A fast map for small key types.

Miscellaneous

Average Accumulator	Accumulator for computing averages.
Hamming StringEnumerator	Enumerate all strings within a given edit distance of a "center string".
Interval Tree Node	An Interval Tree Node that stores intervals explicitely in each node.
Levenshtein StringEnumerator	Enumerate all strings within a given edit distance of a "center string".
Points Only Tree Node	Spec for IntervalTreeNode that stores only the relevant point in each node meaning the endpoint of the interval in the list sorted by endpoints (list2) and only the beginpoint of the interval in the list sorted by beginpoints (list1).
PriorityHeap	Stores the priority data on a heap.

Modifier

Alphabet Expansion	Modifier that adds a character to an alphabet.
ModReverse	Mirrors the characters from begin to end.
ModView	Transforms the characters of the THost string/iterator using a custom function.

Motif Search

CMode	Represents the C ("constant") computation scheme for handling "zero" probabilities.
EPatternBranching	Represents the ePatternBranching algorithm of Davila and Rajasekaran.
PMode	Represents the P computation scheme for handling "zero" probabilities.
Pms1	Represents the Pms1 algorithm developed by Rajasekaran et al.
Pmsp	Represents the Pmsp algorithm of Davila et al.
Projection	Represents the PROJECTION algorithm of Buhler and Tompa.

Parallelism

Equidistant Splitter

Splits an interval into equal-sized subintervals.

Pipelining

Caster	Casts the input type in a specific output type.
Counter	Extends the input stream by a second field which enumerates the elements.
Echoer	Outputs tuples of the echoRepeats last elements of the input stream.
EditEnvironment	Outputs tuples of the tupleLen consecutive elements of the input stream.
Filter	Applies a specific function to the input stream.
Joiner	Joins two or three input streams.
MapperConfig	Configuration of Mapper.
MapperConfigSize	Configuration of Mapper.
MapperSpec	Permutes all elements using a custom destination function.
Namer	Extends the input stream by a second field which names the elements.
PoolConfig	Configuration of Pool.
PoolConfigSize	Configuration of Pool.
PoolSpec	Stores/Retrieves all elements to/from disk.
Sampler	Outputs m-tuples beginning at a position of difference cover DC.
Shifter	Shifts the input stream by delta elements.
SorterConfig	Configuration of Sorter.
SorterConfigSize	Configuration of Sorter.
SorterSpec	Sorts all elements using a custom compare function.
Source	Pipelining adaptor for arbitrary containers or iterators.
Tupler	Outputs tuples of the tupleLen consecutive elements of the input stream.

Proxies

Iterator Proxy

Proxy that is implemented by an iterator.

Random

Beta Pdf	Beta probability density function.
Geometric Pdf	Geometric probability density function with p=0.5. This can be implemented efficiently not using any floating point arithmetics. Just bit operations are needed.
Log-Normal Pdf	Log-normal probability density function.
Mersenne Twister Rng	Mersenne Twister 19937 Random Number Generator
Normal Pdf	Normal probability density function.
Rng Functor	Functor wrapper for random number generation.
Uniform Pdf	Uniform distribution probability density function over a closed interval [min, max].

Scoring

EditDistance	Edit distance scoring scheme.
Score Matrix	A general scoring matrix.
Simple Score	Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.

Searching

AbndmAlgo	Approximate Backward Nondeterministic Dawg Matching algorithm. Approximate string matching using bit parallelism.
AhoCorasick	Multiple exact string matching using Aho-Corasick.
Backtracking	Provides approximate string matching via backtracking on a substring index.
Bfam	Backward Factor Automaton Matching algorithm.
Bfam<Oracle>	Backward Oracle Matching algorithm.
Bfam<Trie>	Backward Suffix Trie Matching algorithm.
BndmAlgo	Backward Nondeterministic Dawg Matching algorithm. Exact string matching using bit parallelism.
DPSearch	A dynamic programming algorithm for approximate string-matching with a user-definable scoring function.
HammingSimpleFinder	A brute force online searching algorithm for approximate string matching with hamming distance.
Hierarchical	By using this Specialization the hierarchical verification is enabled.
Horspool	Exact string matching using Horspool's algorithm (1980).
MultiBfam	Multi-Pattern Backward Factor Automaton Matching.
MultiBfam<Oracle>	Multi-Pattern Backward Factor Automaton Matching using an oracle automaton.
MultipleShiftAnd	Multiple exact string matching using bit parallelism. The total size of the patterns should fit into a computer word.
Myers	Provides fast approximate searching of one string in another using Myer's fast bit-parallel algorithm with application of the Ukkonen-trick.
NonHierarchical	By using this Specialization the hierarchical verification is disabled.
Pex	Provides a fast approximate string matching filter that splits the needle into several pieces that are searched with a multiple exact string matching algorithm and later verified.
Pigeonhole	Provides a fast filter alogrithm that uses the pigeonhole lemma, i.e. if a pattern matches with k errors in the text, every partition into k+1 parts contains one part that matches without error.
SetHorspool	Multiple exact string matching using set horspool algorithm.
ShiftAnd	Exact string matching using bit parallelism. The Shift-And algorithm is applicable to search small patterns in texts using a small alphabet.
ShiftOr	Exact string matching using bit parallelism. The Shift-Or algorithm is applicable to search small patterns in texts using a small alphabet.
Simple Finder	A brute force online searching algorithm.
Swift	Provides a fast filter alogrithm that guarantees to find all regions overlapping with potential ε-matches. An ε-match is a matching region of minimal length and an error rate of at most ε.
SwiftLocal	The specialization for the general swift filter that finds epsilon matches between haystack and needle.
SwiftSemiGlobal	The specialization for the semi-global swift filter that finds regions of the haystack where a needle matches with an error rate less than ε.
WildShiftAnd	Exact string matching with wildcards using bit parallelism. The Shift-And algorithm is applicable to search small patterns in texts using a small alphabet.
WuManber	Online-algorithm for multi-pattern search.

Seed Handling

Chained Seed	Describes a seed with start and end position2 and diagonal upper and lower bounds.
Simple Seed	Describes a seed with start and end position and diagonal upper and lower bounds.

Segments

InfixSegment	An arbitrary segment.
PrefixSegment	First part of a sequence.
SuffixSegment	End part segment of a sequence.

Sequences

ConcatDirect	A string set storing the concatenation of all strings within one string.
ConcatVirtual Iterator	Iterator that sequentially iterates through the elements of a StringSet as if they were directly concatenated, cmp. ConcatDirect.
Dependent	A string set storing references of the strings.
GlobalAlign	Selects a global alignment method to join a Journaled String to a global reference sequence.
GlobalChain	Selects an anchor based method to join a Journaled String to a global reference sequence.
Journaled Set	A string set storing the string as members. It can store a global reference sequence to which all members can be journaled if they are of type Journaled String.
Journaled String	Journaled versions of arbitrary underlying string.
Owner	A string set storing the strings as members.

Strings

Alloc String	Expandable string that is stored on heap.
Array String	Fast, static-size string.
Block String	String optimized for push_back, top, and pop (Stack behaviour).
CStyle String	Allows adaption of strings to C-style strings.
External String	String that is stored in external memory.
File Reader String	Read sequence data from file.
MMap String	String that is stored in external memory. Uses memory mapping.
Packed String	A string that stores as many values in one machine word as possible.
Pizza & Chili String	String used by the Pizza & Chili indices.

SeqAn - Sequence Analysis Library - www.seqan.de