Specializations
Specializations refine Class templates using Template Subclassing.
Allocators
Chunk Pool AllocatorAllocator that pools one or more consecutive memory blocks of a specific size.
Class Pool AllocatorAllocator that pools memory blocks for a specific class.
Multi Pool AllocatorAllocator that pools memory blocks.
Simple AllocatorGeneral purpose allocator.
Single Pool AllocatorAllocator that pools memory blocks of specific size.
Alphabets
AAGroupsDayhoffCompressed amino acid alphabet (Dayhoff).
AAGroupsLiA10Compressed amino acid alphabet (LiA10).
AAGroupsLiB10Compressed amino acid alphabet (LiB10).
AAGroupsMurphyCompressed amino acid alphabet (Murphy).
AAGroupsSeB10Compressed amino acid alphabet (SeB10).
AAGroupsSeB14Compressed amino acid alphabet (SeB14).
AAGroupsSeB6Compressed amino acid alphabet (SeB6).
AAGroupsSeB8Compressed amino acid alphabet (SeB8).
AAGroupsSeV10Compressed amino acid alphabet (SeV10).
AAGroupsSolisD10Compressed amino acid alphabet (SolisD10).
AAGroupsSolisG10Compressed amino acid alphabet (SolisG10).
AminoAcidIupac code for amino acids.
DnaAlphabet for DNA.
Dna5Alphabet for DNA including 'N' character.
IupacIupac code for DNA.
Rna5Rna5 alphabet.
TraceBack Trace back values.
TraceBackGotoh Trace back values for gotoh.
Chaining
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.
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.
FixedGappedShapeA fixed gapped shape.
FixedShapeA fixed length ungapped shape (also called q-gram or k-mer).
GappedShapeA variable gapped shape.
Index_ESAAn index based on an enhanced suffix array.
Index_QGramAn index based on an array of sorted q-grams.
MUMs IteratorIterator to search for all maximum unique matches.
MaxRepeats IteratorIterator to search for all maximal repeats.
MultiMEMs IteratorIterator to search for MultiMEMs.
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.
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.
Miscellaneous
PriorityHeapStores the priority data on a heap.
Modifier
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
MyersUkkonenProvides 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
PamPam scoring matrices.
Score MatrixA general scoring matrix.
Simple ScoreSimple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
Searching
AhoCorasick Multiple exact string matching using Aho-Corasick.
BndmAlgo Backward Nondeterministic Dawg Matching algorithm. Exact string matching using bit parallelism.
BomAlgo Backward Oracle Matching algorithm. Exact string matching using a factor oracle.
DPSearchA dynamic programming algorithm for approximate string-matching with a user-definable scoring function.
Horspool Exact string matching using Horspool's algorithm (1980).
MultipleShiftAnd Multiple exact string matching using bit parallelism. The total size of the patterns should fit into a computer word.
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.
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.
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.
SeqAn - Sequence Analysis Library - www.seqan.de