Specializations
Specializations refine Class templates using Template Subclassing.
Specializations
DPSearch 
Dequeue 
MyersUkkonen 
String 
Alignments
ArrayGapsStores gaps sizes in an array.
SequenceGapsStores gapped sequences as sequences including blank signs.
SumlistGapsStores gaps in a Sumlist.
Allocators
Chunk Pool AllocatorAllocator that pools one or more consecutive memory blocks of a specific size.
Multi Pool AllocatorAllocator that pools memory blocks.
Simple AllocatorGeneral purpose allocator.
Single Pool AllocatorAllocator that pools memory blocks of specific size.
Alphabets
AminoAcidIupac code for amino acids.
DnaAlphabet for DNA.
Dna5Alphabet for DNA including 'N' character.
FiniteA finite alphabet of a fixed size.
IupacIupac code for DNA.
TraceBack Trace back values.
Blast
BasicInfoStores only the basic pieces of information delivered with an alignment in a Blast report.
BlastNFor BlastN Blast reports.
BlastPFor BlastP Blast reports.
FullInfoStores all pieces of information delivered with an alignment in a Blast report.
HitIteratorHit iterator for BlastReport.
HspIteratorHsp iterator for BlastHit.
StoreReportBlastReport specialization. Parses a Blast report and stores all hits and HSPs.
StreamReportBlastReport specialization that works on a file stream (parses hits/HSPs when iterating over them).
Chaining
MultiSeedData structure which represents a seed of multiple sequences.
Score ChainSoPScoring scheme for chaining that uses a special method for scoring the gaps between two fragments.
Score ManhattanScoring scheme for chaining that computes gap scores using manhattan distance.
Score ZeroScoring scheme for chaining that set gap scores to 0
Files
AsyncFile structure supporting synchronous and asynchronous input/output access.
ChainedSplits a large file into a chain of smaller files.
File Reader StringRead sequence data from file.
StripedStripes a file across multiple files.
SyncFile structure supporting synchronous input/output access.
Graph
Adjacency IteratorAdjacency iterator for Graph.
Alignment GraphAn alignment graph.
AutomatonAn 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 IteratorBreath-first search iterator for Graph.
Counting IdManagerId Manager that just counts the number of ids in use.
Dfs Preorder IteratorDepth-first search iterator for Graph.
Directed graphA directed graph that stores the edges in an adjacency list.
Edge IteratorEdge iterator for Graph.
HmmAn Hmm is a directed graph with edges labeled with transition probabilities and emission profiles for each vertex. Vertices correspond to states in an HMM.
OracleA factor oracle.
Out-Edge IteratorOut-edge iterator for Graph.
TreeA 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.
TrieA keyword trie.
Undirected graphAn undirected graph that stores the edges in an adjacency list.
Vertex IteratorVertex iterator for Graph.
Word GraphA special automaton that stores words instead of single characters along its edges.
Holders
Tristate HolderHolder that can be empty, dependent, or owner.
Index
BottomUp IteratorIterator for an efficient postorder depth-first search in a suffix tree.
GappedShapeA fixed gapped shape.
GenericShapeA variable gapped shape.
Index_DFIThe Deferred Frequency Index (see Weese and Schulz, "Efficient string mining under constraints via the deferred frequency index").
Index_ESAAn index based on an enhanced suffix array.
Index_QGramAn index based on an array of sorted q-grams.
Index_WotdAn index based on a lazy suffix tree (see Giegerich et al., "Efficient implementation of lazy suffix trees").
MUMs IteratorIterator to search for all maximum unique matches.
MaxRepeats IteratorIterator to search for all maximal repeats.
MultiMEMs IteratorIterator to search for MultiMEMs.
Pizza & Chili IndexAn adapter for the Pizza & Chili index API.
SimpleShapeA variable length ungapped shape (also called q-gram or k-mer).
SuperMaxRepeats IteratorIterator to search for all supermaximal repeats.
SuperMaxRepeatsFast IteratorIterator to search for all supermaximal repeats (for enh. suffix arrays only).
TopDown IteratorIterator for Suffix Trees that can go down and right beginning from the root.
TopDownHistory IteratorIterator for Suffix Trees that can go down, right, and up.
UngappedShapeA fixed length ungapped shape (also called q-gram or k-mer).
VSTree IteratorAbstract iterator for Suffix Trees.
Iterators
Adaptor IteratorAdapts iterators to Rooted Iterator.
AlignColIteratorIterator for AlignCols pseudo container.
Position IteratorAdapts position to iterator.
SimpleIteratorA simple iterator.
Map
SkiplistGeneral purpose map container.
VectorSetA fast map for small key types.
Miscellaneous
PriorityHeapStores the priority data on a heap.
Modifier
Alphabet ExpansionModifier that adds a character to an alphabet.
ModReverseMirrors the characters from begin to end.
ModViewTransforms 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.
PMS1 Represents the PMS1 algorithm developed by Rajasekaran et al.
PMSP Represents the PMSP algorithm of Davila et al.
PMode Represents the P computation scheme for handling "zero" probabilities.
Projection Represents the PROJECTION algorithm of Buhler and Tompa.
Pattern Matching
HammingHorspoolHamming distance string matching using approximate Boyer-Moore-Horspool algorithm
MyersProvides fast approximate searching of one string in another using Myer's fast bit-parallel algorithm with application of the Ukkonen-trick.
Pipelining
CasterCasts the input type in a specific output type.
CounterExtends the input stream by a second field which enumerates the elements.
EchoerOutputs tuples of the echoRepeats last elements of the input stream.
EditEnvironmentOutputs tuples of the tupleLen consecutive elements of the input stream.
FilterApplies a specific function to the input stream.
JoinerJoins two or three input streams.
MapperConfigConfiguration of Mapper.
MapperConfigSizeConfiguration of Mapper.
MapperSpecPermutes all elements using a custom destination function.
NamerExtends the input stream by a second field which names the elements.
PoolConfigConfiguration of Pool.
PoolConfigSizeConfiguration of Pool.
PoolSpecStores/Retrieves all elements to/from disk.
SamplerOutputs m-tuples beginning at a position of difference cover DC.
ShifterShifts the input stream by delta elements.
SorterConfigConfiguration of Sorter.
SorterConfigSizeConfiguration of Sorter.
SorterSpecSorts all elements using a custom compare function.
SourcePipelining adaptor for arbitrary containers or iterators.
TuplerOutputs tuples of the tupleLen consecutive elements of the input stream.
Proxies
Iterator ProxyProxy that is implemented by an iterator.
Scoring
EditDistanceEdit distance scoring scheme.
PamPam scoring matrices.
Score MatrixA general scoring matrix.
Simple ScoreSimple 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.
BFAMBackward 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.
Hierarchical By using this Specialization the hierarchical verification is enabled.
Horspool Exact string matching using Horspool's algorithm (1980).
MultiBFAMMulti-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.
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.
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 FinderA brute force online searching algorithm.
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.
WuManberOnline-algorithm for multi-pattern search.
Seed Handling
ChainedSeedDescribes a seed with start and end position2 and diagonal upper and lower bounds. Additionaly diagonal segments between start and end position2 are stored.
MemoryManagerIndex Faster than the pointer version but needs data size of at least size_t.
MemoryManagerPointer Datasize of at least 4 bytes. Not suitable for many blocks.
MultiSeedData structure which represents a seed of multiple sequences.
NonScored SeedSetSeedSet that uses seeds without scores.
Scored SeedSetSeedSet that uses scored Seeds.
SimpleSeedDescribes a seed with start and end position and diagonal upper and lower bounds.
Segments
InfixSegmentAn arbitrary segment.
PrefixSegmentFirst part of a sequence.
SuffixSegmentEnd part segment of a sequence.
Sequences
ConcatDirectA string set storing the concatenation of all strings within one string.
DependentA string set storing references of the strings.
OwnerA string set storing the strings as members.
Strings
Alloc StringExpandable string that is stored on heap.
Array StringFast but non-expandable string.
Block StringString optimized for push_back, top, and pop (Stack behaviour).
CStyle StringAllows adaption of strings to C-style strings.
External StringString that is stored in external memory.
File Reader StringRead sequence data from file.
Packed StringA string that stores as many values in one machine word as possible.
Pizza & Chili StringString used by the Pizza & Chili indices.
SeqAn - Sequence Analysis Library - www.seqan.de