Tags
This section describes the tags that can be used in SeqAn algorithms and data structures.
Tags
Alignment Graph CombinationA tag to specify how to combine alignment graphs.
Alignment Graph FormatA file format to write an alignment graph.
Allocator UsageThe purpose of an allocated memory block.
Consensus CallingA tag that specifies how to call the consensus.
DefaultTag that specifies default behavior.
Distance CalculationA tag to specify how to calculate distance matrices.
DotDrawingSwitch to trigger drawing in dot format.
File FormatA file format.
Global Alignment AlgorithmsGlobal alignment algorithm used by globalAlignment.
Graph IteratorA specification of the iterator to traverse a graph.
HammingDistanceSwitch to trigger Hamming distance, which is a measure of character substitutions.
Iterator SpecSpecifies the kind of an iterator.
LevenshteinDistanceSwitch to trigger Levenshtein distance, which is a measure of edit operations (character substitutions, deletions or insertions).
Local Alignment AlgorithmsLocal alignment algorithm used by localAlignment.
Logical ValuesTag that represents true and false.
Move SwitchSwitch to force move.
NothingTag that represents an absent parameter or an absent type.
Overflow StrategyThe strategy for resizing containers.
Prefix OrderSpecify whether a prefix is smaller or greater.
Segment Match GenerationA tag that specifies how to generate segment matches.
Upgma ConfiguratorA tag to configure the guide tree construction.
Index
ESA Index FibresTag to select a specific fibre (e.g. table, object, ...) of an ESA index.
EmptyEdgesConsider a suffix tree with leaves for every suffix.
HideEmptyEdgesConsider a suffix tree with no empty edges (default behaviour).
Index Find AlgorithmTag to specify the index search algorithm.
Pizza & Chili Index FibresTag to select a specific fibre (e.g. table, object, ...) of a Pizza & Chili Index index.
Pizza & Chili Index TagsTag specifying the Pizza & Chili library to use.
PostorderPostorder depth-first search.
PostorderEmptyEdgesPostorder depth-first search in a suffix tree with leaves for every suffix.
PreorderPreorder depth-first search.
PreorderEmptyEdgesPreorder depth-first search in a suffix tree with leaves for every suffix.
QGram Index FibresTag to select a specific fibre (e.g. table, object, ...) of a q-gram Index.
Motif Search
OMOPSRepresents the One or More Occurences Per Sequence model.
OOPSRepresents the One Occurrence Per Sequence model.
TCMRepresents the Two-Component-Mixture Sequence model.
ZOOPSRepresents the Zero or One Occurence Per Sequence model.
Searching
Index Find AlgorithmTag to specify the index search algorithm.
Seed Handling
Seed AddingThe algorithm used to add a seed to a SeedSet.
Seed ExtensionThe algorithms used to extend a seed.
SeedSet Tags for the behaviour of a SeedSet
Strings
ExternalConfigStandard configuration for the External String.
ExternalConfigLargeLarge size type configuration for the External String.
ExternalConfigSizeArbitrary size type configuration for the External String.
SeqAn - Sequence Analysis Library - www.seqan.de