Classes
This section lists the main classes provided by SeqAn.
Many of these classes are templates that can be specialized using Template Subclassing.
See the section Specializations for a list of these specializations.
Classes
| A structure to select a tag from a TagList. |
Aggregates
| Stores references to two arbitrary objects. | |
| Stores references to three arbitrary objects. | |
| Stores references to five arbitrary objects. | |
| Stores two arbitrary objects. | |
| Stores three arbitrary objects. | |
| A plain fixed-length string. |
Alignments
| An alignment of sequences. | |
| Pseudo columns container for row-based alignment classes. | |
| The AlignConfig class encapsulates how DP is carried out. It indicates at what ends gaps are free, the so-called free ends-space alignments. | |
| A type for ungapped, pairwise segment matches. | |
| Stores the position of an alignment character in sequence-space and in gap-space. | |
| Stores the gaps in a gapped sequences. |
Basic
| Manager for allocated memory. | |
| Manages relationship to another object. | |
| Iterator that is used to traverse containers. | |
| Comparator for lexical comparison. | |
| Emulates object of another class. | |
| Implementation for "simple" types. | |
| Emulates standard conform allocator. |
Blast
| Object for storing Blast hits. | |
| Object for storing Blast HSPs. | |
| Object for storing Blast report information. |
Fragment Store
| Stores alignment qualities. | |
| Stores a 2-dimensional visible layout of a multi-read alignment. | |
| Represents an alignment between read and contig. | |
| Represents a file containing contigs. | |
| Represents a single contig. | |
| Multi-Container to store contigs, reads and a multiple alignment between them. | |
| Represents a fragment library. | |
| Represents a mate-pair. | |
| Stores a mapping from names to ids. | |
| Represents a single read (without sequence). |
Graph
| The EdgeStump class encapsulates a single edge. It represents either a list node in the adjacency list of a graph or an array field if edges are stored in an array. | |
| An external property map. | |
| Generic graph. | |
| Id manager that provides unique ids for vertices and edges. | |
| An internal property map using member ids. | |
| An internal property map using pointer to members. | |
| An internal property map using raw pointer to members. |
Index
| A structure to define a fixed gapped shape. | |
| Contains preprocessing data of a fixed text. Allows fast dictionary look-up and advanced computations. | |
| Stores hash value and shape for an ungapped or gapped q-gram. |
Input/Output
| Associated with an asynchronous I/O request. | |
| Auto-detects and stores a file format. | |
| Represents a file. | |
| Object that stores a file format. |
Map
| Set/dictionary container. |
MarkovModel
| Gives a suitable representation of a Marcov Chain. |
Miscellaneous
| Stores information for a specific command line option. | |
| Stores multiple CommandLineOption objects and parses the command line arguments for these options. | |
| A double-ended queue implementation on top of a String. | |
| A simple record type that stores an interval and a cargo value. | |
| A datastructure that efficiently stores intervals. | |
| Element of IntervalTree. | |
| Stores the information necessary for local alignment dynamic programming. | |
| A simple n-dimensional matrix type. | |
| Simple record class storing a point (one-value interval) and a cargo. | |
| Stores items in such a way that the item with the highest priority is at the top. | |
| A scoring scheme. |
Modifier
| Functor that returns the complement nucleotide to a given nucleotide. | |
| Functor that converts a | |
| Functor that returns the lower case character to a given character. | |
| Functor that returns the upper case character to a given character. | |
| Modifies value types. | |
| Allows to modify arbitrary iterators by specializing what differs from an origin. | |
| Allows to modify arbitrary strings by specializing what differs from an origin. |
Motif Search
| Holds a collection of objects of a specific type, where each object represents the frequency (absolute or relative probability) of a particular residue which is a member of a fixed sequence alphabet. | |
| Holds the algorithm parameter values and the motif instance(s) found by the appropriate motif discovery algorithm. | |
| Holds the pseudocounts for each residue of a given sequence alphabet. |
Pipelining
| Pipes are pop-passive pipeline modules. | |
| Pools are push- and pop-passive pipeline modules. |
Searching
| Holds the haystack and a current search context. | |
| Holds the needle and preprocessing data (depends on algorithm). |
Seed Handling
| Saves and manages data using IDs. | |
| Class used to save additional data together with a MemoryManager. | |
| Describes a seed. | |
| Manages seeds for local chaining and merging algorithms. |
Sequences
| A sequence class that virtually concatenates all sequences in a StringSet. | |
| Stores the gaps in a gapped sequences. | |
| A contiguous part of a sequence. | |
| General purpose container for sequences. | |
| A container class for a set of strings. |
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