Tags

| Tags This section describes the tags that can be used in SeqAn algorithms and data structures. Tags
Alignment Graph Combination | A tag to specify how to combine alignment graphs.
Alignment Graph Format | A file format to write an alignment graph.
Allocator Usage | The purpose of an allocated memory block.
Consensus Calling | A tag that specifies how to call the consensus.
Default | Tag that specifies default behavior.
Distance Calculation | A tag to specify how to calculate distance matrices.
DotDrawing | Switch to trigger drawing in dot format.
File Format | A file format.
FindInfix | Find needle as a substring of haystack (infix search).
FindPrefix | Find needle as a prefix of the haystack (prefix serach)
Global Alignment Algorithms | Global alignment algorithm used by globalAlignment.
Graph Iterator | A specification of the iterator to traverse a graph.
HammingDistance | Switch to trigger Hamming distance, which is a measure of character substitutions.
Iterator Spec | Specifies the kind of an iterator.
LevenshteinDistance | Switch to trigger Levenshtein distance, which is a measure of edit operations (character substitutions, deletions or insertions).
Local Alignment Algorithms | Local alignment algorithm used by localAlignment.
Logical Values | Tag that represents true and false.
Move Switch | Switch to force move.
Nothing | Tag that represents an absent parameter or an absent type.
Overflow Strategy | The strategy for resizing containers.
Prefix Order | Specify whether less-than or greather-than comparison is meant.
Segment Match Generation | A tag that specifies how to generate segment matches.
TagList | A structure to represent a list of tags.
Upgma Configurator | A tag to configure the guide tree construction.
Fragment Store
sortAlignedRead Tags | Tag to select a specific field to stably sort the alignedReadStore by.
Index
ESA Index Fibres | Tag to select a specific fibre (e.g. table, object, ...) of an ESA index.
EmptyEdges | Consider a suffix tree with leaves for every suffix.
HideEmptyEdges | Consider a suffix tree with no empty edges (default behaviour).
Index Find Algorithm | Tag to specify the index search algorithm.
Pizza & Chili Index Fibres | Tag to select a specific fibre (e.g. table, object, ...) of a Pizza & Chili Index index.
Pizza & Chili Index Tags | Tag specifying the Pizza & Chili library to use.
Postorder | Postorder depth-first search.
PostorderEmptyEdges | Postorder depth-first search in a suffix tree with leaves for every suffix.
Preorder | Preorder depth-first search.
PreorderEmptyEdges | Preorder depth-first search in a suffix tree with leaves for every suffix.
QGram Index Fibres | Tag to select a specific fibre (e.g. table, object, ...) of a q-gram Index.
WOTD Index Fibres | Tag to select a specific fibre (e.g. table, object, ...) of an IndexWotd index.
Miscellaneous
IntervalTree Centers | Tag to select a specific way to compute the center of an interval tree node.
IntervalTree Node Types | Tags to select the node type for IntervalTree.
Motif Search
Omops | Represents the One or More Occurences Per Sequence model.
Oops | Represents the One Occurrence Per Sequence model.
Tcm | Represents the Two-Component-Mixture Sequence model.
Zoops | Represents the Zero or One Occurence Per Sequence model.
Random
MeanStdDev | Tag to specify that the given parameters are mean an standard deviation of the lognormal distribution.
MuSigma | Tag to specify that the given parameters are mu and sigma of the underlying normal distribution for lognormal distributions.
Scoring
Simple | Tag for the Score to mark it as a simple score.
Searching
Index Find Algorithm | Tag to specify the index search algorithm.
Seed Handling
Seed Adding | The algorithm used to add a seed to a SeedSet.
Seed Extension | The algorithms used to extend a seed.
SeedSet | Tags for the behaviour of a SeedSet
Strings
ExternalConfig | Standard configuration for the External String.
ExternalConfigLarge | Large size type configuration for the External String.
ExternalConfigSize | Arbitrary size type configuration for the External String.
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2012/03/14 16:34:45