Spec PigeonholePattern

Pigeonhole-based pattern. Must be used together with PigeonholeFinder.

/*!
 * @class PigeonholePattern
 * 
 * @extends Pattern
 * 
 * @headerfile <seqan/index/find_pigeonhole.h>
 * 
 * @brief Pigeonhole-based pattern. Must be used together with @link
 *        PigeonholeFinder @endlink.
 * 
 * @signature template <typename THaystack, typename TSpec> class
 *            Pattern<TIndex, Pigeonhole<TSpec> >;
 * 
 * @tparam TSpec Specifies the type of pigeonhole filter.
 * @tparam TIndex A q-gram index of needle(s) that should be searched for.
 *                Types: @link IndexQGram @endlink
 * 
 * See @link PigeonholeFinder @endlink for more information on the algorithm.
 * 
 * @see PigeonholeFinder
 * 
 * @var PigeonholeParameters PigeonholePattern::parameters;
 * 
 * @brief The pigeonhole parameters to use for configuration.
 * 
 * @fn PigeonholePattern#maskPatternSequence
 * 
 * @headerfile <seqan/index/find_pigeonhole.h>
 * 
 * @brief Mask and unmask pattern sequence.
 * 
 * @note Disabling sequences in the pigeonhole filter requires the
 *       <tt>ONE_PER_DIAGONAL</tt> heuristic.
 * 
 * @signature void maskPatternSequence(pattern, seqNo, enable);
 * 
 * @param[in,out] pattern The PigeonholePattern to update.
 * @param[in] seqNo Index of the sequence to disable/enable.
 * @param[in] enable A <tt>bool</tt> that indicates whether hits are to be
 *                   generated for the given sequence.
 * 
 * @fn PigeonholePattern#getMaxDeviationOfOrder
 * 
 * @headerfile <seqan/index/find_pigeonhole.h>
 * 
 * @brief Returns the maximal out-of-order distance of adjacent hits.
 * 
 * @signature TSize getMaxDeviationOfOrder(pattern);
 * 
 * @param[in] pattern A PigeonholeFinder.
 * 
 * @return TSize Returns the maximal distance two adjacent hits can have which
 *               are not in increasing order. <tt>TSize</tt> is the size type of
 *               the underlying index.
 */