Spec FMIndex

An index based on the Burrows-Wheeler transform.

/*!
 * @class FMIndex
 * 
 * @implements StringTrieConcept
 * 
 * @extends Index
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief An index based on the Burrows-Wheeler transform.
 * 
 * @signature template <typename TText[, typename TSpec[, typename TConfig]]>
 *            class Index<TText, FMIndex<TSpec, TConfig> >;
 * 
 * @tparam TText The text type. Types: @link String @endlink, @link StringSet
 *               @endlink
 * @tparam TSpec FM index specialisation, defaults to <tt>void</tt>.
 * @tparam TConfig A config object which determines the data types of the
 *                 different fibres, defaults to
 *                 <tt>FMIndexConfig&lt;TSpec&gt;</tt>.
 * 
 * @section Structure
 * 
 * The FM index consists of various @link Fibre @endlink of which the most
 * important ones are the compressed suffix array and the LF table, which
 * provides all necessary information for the LF mapping.
 * 
 * @fn FMIndex#indexLF
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief A shortcut for <tt>getFibre(index, FibreLF())</tt>.
 * 
 * @signature TFibre indexLF(index);
 * 
 * @param[in] index The FM index.
 * 
 * @return TFibre A reference to the @link FMIndexFibres#FibreLF @endlink.
 * 
 * @fn FMIndex#toSuffixPosition
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief This function computes the position of a specified position in the
 *        compressed suffix array (additionally containing entries for the
 *        sentinels). The returned position corresponds to the suffix array of
 *        the original text without sentinels.
 * 
 * @signature TSAValue toSuffixPosition(index, pos, offset);
 * 
 * @param[in] index The FM index.
 * @param[in] pos The position in the suffix array of the FM index (with
 *                sentinels). Types: @link UnsignedIntegerConcept @endlink
 * @param[in] offset The number of sequences in the original text. Types: @link
 *                   UnsignedIntegerConcept @endlink
 * 
 * @return TSAValue The function function computes the position of a specified
 *                  position in the compressed suffix array (additionally
 *                  containing entries for the sentinels). The returned position
 *                  corresponds to the suffix array of the original text without
 *                  sentinels. The return type is @link SAValue
 *                  @endlink&lt;@link Index @endlink&lt;TText, FMIndex&lt;TSpec,
 *                  TConfig&gt; &gt; &gt;::Type
 * 
 * @fn FMIndex#begin
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief Returns an iterator pointing to the root node of the virtual prefix
 *        trie of the reversed text of the index.
 * 
 * @signature TIterator begin(index, tag);
 * 
 * @param[in] index The index to be traversed.
 * @param[in] tag The specialisation of the iterator to be returned by the
 *                function. Types: VSTree Iterator
 * 
 * @return TIterator Returns an iterator pointing to the root node of the
 *                   virtual prefix trie of the reversed text of the the index.
 *                   Types: <tt>The result of Iterator&lt;Index&lt;TText,
 *                   TIndexSpec&gt;, TSpec&gt;::Type</tt>
 */