Class
MsaOptionsConfiguration for globalMsaAlignment
Configuration for globalMsaAlignment
Defined in | <seqan/graph_msa.h> |
---|---|
Signature |
template <typename TAlphabet, typename TScore>
struct MsaOptions;
|
Member Function Overview
-
MsaOptions::MsaOptions();
Default constructor.
Member Variable Overview
-
unsigned MsaOptions::bandWidth
Band width for banded alignment. Min value: 2. -
unsigned MsaOptions::build
Methods for computing guide tre. -
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>. -
unsigned MsaOptions::outputFormat
Output Format (0 - FASTA, 1 MSF, default: 0). -
unsigned MsaOptions::pairwiseAlignmentMethod
Methods for computing pairwise alignment. -
bool MsaOptions::rescore
Whether or not to rescore segment matches after refinment (default: true). -
TScore MsaOptions::sc
The Score object to use.
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.