MsaOptions - SeqAn API Documentation

# 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

- `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.

#### Dox Sources

    /*!
     * @class MsaOptions
     *
     * @headerfile <seqan/graph_msa.h>
     *
     * @brief Configuration for @link globalMsaAlignment @endlink
     *
     * @signature template <typename TAlphabet, typename TScore> struct MsaOptions;
     *
     * @tparam TAlphabet The alphabet type to use.
     * @tparam TScore The @link Score @endlink type to use.
     *
     * @fn MsaOptions::MsaOptions
     *
     * @brief Default constructor.
     *
     * @signature MsaOptions::MsaOptions();
     *
     * @var bool MsaOptions::rescore;
     *
     * @brief Whether or not to rescore segment matches after refinment (default:
     *        <tt>true</tt>).
     *
     * @var unsigned MsaOptions::outputFormat;
     *
     * @brief Output Format (<tt>0</tt> - FASTA, <tt>1</tt> MSF, default:
     *        <tt>0</tt>).
     *
     * @var TScore MsaOptions::sc;
     *
     * @brief The @link Score @endlink object to use.
     *
     * @var unsigned MsaOptions::build;
     *
     * @brief 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.
     *
     * @var TUnsignedString MsaOptions::method;
     *
     * @brief All methods to compute segment matches, of Type
     *        <tt>String&lt;unsigned&gt;</tt>.
     *
     * 0 global alignment, 1 local alignments, 2 overlap alignments, 3 longest
     * common subsequence
     *
     * @var unsigned MsaOptions::isDefaultPairwiseAlignment;
     *
     * @brief Whether or not to use default strategy for choosing pairwise alignment
     *        methods.
     *
     * @var unsigned MsaOptions::pairwiseAlignmentMethod;
     *
     * @brief Methods for computing pairwise alignment.
     *
     * 0 unspecified, 1 unbanded, 2 banded Default: 0
     *
     * @var unsigned MsaOptions::bandWidth;
     *
     * @brief Band width for banded alignment. Min value: <tt>2</tt>.
     */