Tags
This section describes the tags that can be used in SeqAn algorithms and data structures.
Aggregates

BitPacked | Tag to mark a bit-packed specialization that avoids to waste bits.
Pack | Tag to mark a packed specialization that disables address alignment for members.

Alignments

Alignment Graph Combination | A tag to specify how to combine alignment graphs.
Distance Calculation | A tag to specify how to calculate distance matrices.
Join Strategies | Tags used for selecting journaling strategies when joining a Journaled String to a global reference sequence.
Pairwise Global Alignment Algorithms | Tags used for selecting pairwise global alignment algorithms.
Pairwise Local Alignment Algorithms | Tags used for selecting pairwise global alignment algorithms.
Segment Match Generation | A tag that specifies how to generate segment matches.
Upgma Configurator | A tag to configure the guide tree construction.

BAM I/O

Bam | Tag for identifying the BAM format.
Sam | Tag for identifying the SAM format.

Basic

Default | Tag that specifies default behavior.
HammingDistance | Switch to trigger Hamming distance, which is a measure of character substitutions.
LevenshteinDistance | Switch to trigger Levenshtein distance, which is a measure of edit operations (character substitutions, deletions or insertions).
Move Switch | Switch to force move.
Nothing | Tag that represents an absent parameter or an absent type.
TagList | A structure to represent a list of tags.

Consensus

Consensus Calling | A tag that specifies how to call the consensus.

Fragment Store

sortAlignedRead Tags | Tag to select a specific field to stably sort the alignedReadStore by.

Fundamental

Tag | Template for tag definition.

Graph

Graph Iterator | A specification of the iterator to traverse a graph.

Index

BottomUp | Tag that specifies a VSTree Iterator to traverse the virtual string tree from the root towards the leafs.
CompressText | Tag to select a FM index variant that can be used such that it is not necessary to store the text after index construction. This index is very space efficient.
CompressedSA Fibres | Tag to select a specific fibre of a CompressedSA.
DFS Order | Pre/postorder selection for depth-first search.
ESA Index Fibres | Tag to select a specific fibre (e.g. table, object, ...) of an ESA index.
FM Index Fibres | Tag to select a specific fibre of a FMIndex.
LF Table Fibres | Tag to select a specific fibre of a FMIndex.
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.
PrefixSumTable Fibres | Tag to select a specific fibre of a CompressedSA.
QGram Index Fibres | Tag to select a specific fibre (e.g. table, object, ...) of a q-gram Index.
RankSupportBitString Fibres | Tag to select a specific fibre (e.g. table, object, ...) of a RankSupportBitString.
SBM | Tag that specifies the FMIndex to use a StringSet of rank support bis strings as the occurrence table.
SparseString Fibres | Tag to select a specific fibre of a SparseString.
TopDown | Tag that specifies a VSTree Iterator to traverse the virtual string tree from the root towards the leafs.
WOTD Index Fibres | Tag to select a specific fibre (e.g. table, object, ...) of an IndexWotd index.
WT | Tag that specifies the FMIndex to use a wavelet tree as the occurrence table.

Input/Output

Alignment Graph Format | A file format to write an alignment graph.
DotDrawing | Switch to trigger drawing in dot format.
File Format | A file format.
Stream Feature | Tag to select a given feature for querying in HasStreamFeature.

Iteration

Iterator Spec | Specifies the kind of an iterator.

Memory

Allocator Usage | The purpose of an allocated memory block.

Metaprogramming

Case | Metaprogramming case expression.
Logical Values | Tag that represents true and false.
NilCase | Metaprogramming default: case expression.

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.

Parallelism

Parallel | Tag to select a parallel implementation of an algorithm.
Serial | Tag to select a non-parallel implementation of an algorithm.

Random

Lognormal Construction | Specify parameters for lognormal distribution construction.

RightArrayBinaryTree

RightArrayBinaryTree Fibres | Tag to select a specific fibre (e.g. table, object, ...) of a RightArrayBinaryTree.

Searching

FindInfix | Find needle as a substring of haystack (infix search).
FindPrefix | Find needle as a prefix of the haystack (prefix serach)
Index Find Algorithm | Tags to specialise the search strategies.

Seed Handling

Global Chaining | Tags for selecting the global chaining algorithm.
Local Chaining | The local chaining algorithms to use when adding a seed to a SeedSet.
Seed Extension | The algorithms used to extend a seed.

SentinelRankDictionary

SentinelRankDictionary Fibres | Tag to select a specific fibre (e.g. table, object, ...) of a SentinelRankDictionary.

Sequences

Overflow Strategy | The strategy for resizing containers.
Prefix Order | Specify whether less-than or greather-than comparison is meant.

Spec: WaveletTree

WaveletTree Fibres | Tag to select a specific fibre (e.g. table, object, ...) of a WaveletTree.

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 @2014/10/13 16:12:56