Class MsaOptions
Configuration for globalMsaAlignment

Defined in <seqan/graph_msa.h>
Signature template <typename TAlphabet, typename TScore> struct MsaOptions;

Template Parameters

TAlphabet The alphabet type to use.
TScore The Score type to use.

Member Function Overview

Member Variable Overview

Member Functions Detail


Default constructor.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

Member Variables Detail

unsigned MsaOptions::bandWidth

Band width for banded alignment. Min value: 2.

unsigned MsaOptions::build

Methods for computing guide tre.

0 Neighbor-joining, 1 UPGMA single linkage, 2 UPGMA complete linkage, 3 UPGMA average linkage, 4 UPGMA weighted average linkage.

unsigned MsaOptions::isDefaultPairwiseAlignment

Whether or not to use default strategy for choosing pairwise alignment methods.

TUnsignedString MsaOptions::method

All methods to compute segment matches, of Type String<unsigned>.

0 global alignment, 1 local alignments, 2 overlap alignments, 3 longest common subsequence

unsigned MsaOptions::outputFormat

Output Format (0 - FASTA, 1 MSF, default: 0).

unsigned MsaOptions::pairwiseAlignmentMethod

Methods for computing pairwise alignment.

0 unspecified, 1 unbanded, 2 banded Default: 0

bool MsaOptions::rescore

Whether or not to rescore segment matches after refinment (default: true).

TScore MsaOptions::sc

The Score object to use.