Specializations
Specializations refine Class templates using Template Subclassing.
Allocators
Allocator that pools one or more consecutive memory blocks of a specific size. | |
Allocator that pools memory blocks for a specific class. | |
Allocator that pools memory blocks. | |
General purpose allocator. | |
Allocator that pools memory blocks of specific size. |
Alphabets
Compressed amino acid alphabet (Dayhoff). | |
Compressed amino acid alphabet (LiA10). | |
Compressed amino acid alphabet (LiB10). | |
Compressed amino acid alphabet (Murphy). | |
Compressed amino acid alphabet (SeB10). | |
Compressed amino acid alphabet (SeB14). | |
Compressed amino acid alphabet (SeB6). | |
Compressed amino acid alphabet (SeB8). | |
Compressed amino acid alphabet (SeV10). | |
Compressed amino acid alphabet (SolisD10). | |
Compressed amino acid alphabet (SolisG10). | |
Iupac code for amino acids. | |
Alphabet for DNA. | |
Alphabet for DNA including 'N' character. | |
Iupac code for DNA. | |
Rna5 alphabet. | |
Trace back values. | |
Trace back values for gotoh. |
Chaining
Scoring scheme for chaining that uses a special method for scoring the gaps between two fragments. | |
Scoring scheme for chaining that computes gap scores using manhattan distance. | |
Scoring scheme for chaining that set gap scores to 0 |
Files
File structure supporting synchronous and asynchronous input/output access. | |
Splits a large file into a chain of smaller files. | |
Read sequence data from file. | |
Stripes a file across multiple files. | |
File structure supporting synchronous input/output access. |
Graph
Adjacency iterator for Graph. | |
An alignment graph. | |
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. | |
Breath-first search iterator for Graph. | |
Id Manager that just counts the number of ids in use. | |
Depth-first search iterator for Graph. | |
A directed graph that stores the edges in an adjacency list. | |
Edge iterator for Graph. | |
A factor oracle. | |
Out-edge iterator for Graph. | |
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. | |
A keyword trie. | |
An undirected graph that stores the edges in an adjacency list. | |
Vertex iterator for Graph. | |
A special automaton that stores words instead of single characters along its edges. |
Holders
Holder that can be empty, dependent, or owner. |
Index
Iterator for an efficient postorder depth-first search in a suffix tree. | |
A fixed gapped shape. | |
A fixed length ungapped shape (also called q-gram or k-mer). | |
A variable gapped shape. | |
An index based on an enhanced suffix array. | |
An index based on an array of sorted q-grams. | |
Iterator to search for all maximum unique matches. | |
Iterator to search for all maximal repeats. | |
Iterator to search for MultiMEMs. | |
A variable length ungapped shape (also called q-gram or k-mer). | |
Iterator to search for all supermaximal repeats. | |
Iterator to search for all supermaximal repeats (for enh. suffix arrays only). | |
Iterator for Suffix Trees that can go down and right beginning from the root. | |
Iterator for Suffix Trees that can go down, right, and up. | |
Abstract iterator for Suffix Trees. |
Iterators
Adapts iterators to Rooted Iterator. | |
Iterator for AlignCols pseudo container. | |
Adapts position to iterator. | |
A simple iterator. |
Miscellaneous
Stores the priority data on a heap. |
Modifier
Mirrors the characters from begin to end. | |
Transforms the characters of the |
Motif Search
Represents the C ("constant") computation scheme for handling "zero" probabilities. | |
Represents the ePatternBranching algorithm of Davila and Rajasekaran. | |
Represents the PMS1 algorithm developed by Rajasekaran et al. | |
Represents the PMSP algorithm of Davila et al. | |
Represents the P computation scheme for handling "zero" probabilities. | |
Represents the PROJECTION algorithm of Buhler and Tompa. |
Pattern Matching
Provides fast approximate searching of one string in another using Myer's fast bit-parallel algorithm with application of the Ukkonen-trick. |
Pipelining
Casts the input type in a specific output type. | |
Extends the input stream by a second field which enumerates the elements. | |
Outputs tuples of the | |
Outputs tuples of the | |
Applies a specific function to the input stream. | |
Joins two or three input streams. | |
Configuration of Mapper. | |
Configuration of Mapper. | |
Permutes all elements using a custom destination function. | |
Extends the input stream by a second field which names the elements. | |
Configuration of Pool. | |
Configuration of Pool. | |
Stores/Retrieves all elements to/from disk. | |
Outputs m-tuples beginning at a position of difference cover DC. | |
Shifts the input stream by | |
Configuration of Sorter. | |
Configuration of Sorter. | |
Sorts all elements using a custom compare function. | |
Pipelining adaptor for arbitrary containers or iterators. | |
Outputs tuples of the |
Proxies
Proxy that is implemented by an iterator. |
Scoring
Pam scoring matrices. | |
A general scoring matrix. | |
Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps. |
Searching
Multiple exact string matching using Aho-Corasick. | |
Backward Nondeterministic Dawg Matching algorithm. Exact string matching using bit parallelism. | |
Backward Oracle Matching algorithm. Exact string matching using a factor oracle. | |
A dynamic programming algorithm for approximate string-matching with a user-definable scoring function. | |
Exact string matching using Horspool's algorithm (1980). | |
Multiple exact string matching using bit parallelism. The total size of the patterns should fit into a computer word. | |
Multiple exact string matching using set horspool algorithm. | |
Exact string matching using bit parallelism. The Shift-And algorithm is applicable to search small patterns in texts using a small alphabet. | |
Exact string matching using bit parallelism. The Shift-Or algorithm is applicable to search small patterns in texts using a small alphabet. | |
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
An arbitrary segment. | |
First part of a sequence. | |
End part segment of a sequence. |
Sequences
A string set storing the concatenation of all strings within one string. | |
A string set storing references of the strings. | |
A string set storing the strings as members. |
Strings
Expandable string that is stored on heap. | |
Fast but non-expandable string. | |
String optimized for push_back, top, and pop (Stack behaviour). | |
Allows adaption of strings to C-style strings. | |
String that is stored in external memory. | |
Read sequence data from file. | |
A string that stores as many values in one machine word as possible. |
SeqAn - Sequence Analysis Library - www.seqan.de