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.

Profile Alignment

ProfileSeq Score | Score for profile-to-sequence alignments.
ProfileSeqFrac Score | Score for profile-to-sequence alignments.

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 |
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. A string that stores as many values in one machine word as possible.
Packed String | A string that stores as many values in one machine word as possible. 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

Page built @2014/10/13 16:12:56