Specializations
Specializations refine Class templates using Template Subclassing.
Aggregates

Bit Compressed 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.

Alignments

AnchorGaps | Stores gaps anchors of the first characters behind gaps.
ArrayGaps | Stores gaps sizes in an array.
ExactFragment | A type for ungapped, pairwise segment matches.
ExactReversableFragment | A type for ungapped, pairwise segment matches that may be in reverse orientation.
SumlistGaps | Stores gaps in a Sumlist.

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.

Blast

BasicInfo | Stores only the basic pieces of information delivered with an alignment in a Blast report.
BlastN | For BlastN Blast reports.
BlastP | For BlastP Blast reports.
FullInfo | Stores all pieces of information delivered with an alignment in a Blast report.
HitIterator | Hit iterator for BlastReport.
HspIterator | Hsp iterator for BlastHit.
StoreReport | BlastReport specialization. Parses a Blast report and stores all hits and HSPs.
StreamReport | BlastReport specialization that works on a file stream (parses hits/HSPs when iterating over them).

Chaining

MultiSeed | Data structure which represents a seed of multiple sequences.
Score ChainSoP | Scoring scheme for chaining that uses a special method for scoring the gaps between two fragments.
Score Manhattan | Scoring scheme for chaining that computes gap scores using manhattan distance.
Score Zero | Scoring scheme for chaining that set gap scores to 0

Files

Async | File structure supporting synchronous and asynchronous input/output access.
Chained | Splits a large file into a chain of smaller files.
File Reader String | Read sequence data from file.
Striped | Stripes a file across multiple files.
Sync | File structure supporting synchronous input/output access.

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

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.
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 | An index based on an enhanced suffix array.
IndexQGram | An index based on an array of sorted q-grams.
IndexWotd | An index based on a lazy suffix tree (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.
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 suffix trees that can go down and right beginning from the root.
TopDownHistory Iterator | Iterator for suffix trees 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.

Iterators

Adaptor Iterator | Adapts iterators to Rooted Iterator.
AlignColIterator | Iterator for AlignCols pseudo container.
Position Iterator | Adapts position to iterator.
SimpleIterator | A simple iterator.

Map

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

Miscellaneous

Interval Tree Node | An Interval Tree Node that stores intervals explicitely in each node.
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.

Pattern Matching

Myers | Provides fast approximate searching of one string in another using Myer's fast bit-parallel algorithm with application of the Ukkonen-trick.

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

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.
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.
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 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

ChainedSeed | Describes 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.
MultiSeed | Data structure which represents a seed of multiple sequences.
NonScored SeedSet | SeedSet that uses seeds without scores.
Scored SeedSet | SeedSet that uses scored Seeds.
SimpleSeed | 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.
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.

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