Class MsaOptions

Configuration for globalMsaAlignment

/*!
 * @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
 */