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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