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

MsaOptions::MsaOptions();

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.