Class SparseString

A string storing only a fraction of the values of the original string.

/*!
 * @class SparseString
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief A string storing only a fraction of the values of the original string.
 * 
 * @signature template <typename TValueString, typename TSpec> class
 *            SparseString;
 * 
 * @tparam TSpec The specialisation tag. Default: void.
 * @tparam TValueString The type of the @link String string @endlink containing
 *                      the values.
 * 
 * @fn SparseString#clear
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief Resets the @link SparseString @endlink.
 * 
 * @signature void clear(sparseString);
 * 
 * @param[in,out] sparseString The @link SparseString @endlink to be cleared.
 * 
 * @fn SparseString#empty
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief Returns whether or not the @link SparseString @endlink is empty.
 * 
 * @signature bool empty(sparseString);
 * 
 * @param[in] sparseString The SparseString to be checked.
 * 
 * @return bool <tt>true</tt> if there are no elements in the sparse string and
 *              <tt>false</tt> otherwise.
 * 
 * @fn SparseString#getValue
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief Returns the value of a SparseString.
 * 
 * @signature TValue getValue(sparseString, pos);
 * 
 * @param[in] sparseString The @link SparseString @endlink.
 * @param[in] pos The position at which a value should be assign to the sparse
 *                string. Types: @link UnsignedIntegerConcept @endlink
 * 
 * @return TValue The type @link GetValue @endlink of @link SparseString
 *                @endlink is returned.
 * 
 * @fn SparseString#value
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief Returns the value of a @link SparseString @endlink.
 * 
 * @signature TReference value(sparseString, pos);
 * 
 * @param[in] sparseString The @link SparseString @endlink.
 * @param[in] pos The position at which a value should be assign to the sparse
 *                string. Types: @link UnsignedIntegerConcept @endlink
 * 
 * @return TReference The type @link Reference @endlink of @link SparseString
 *                    @endlink is returned.
 * 
 * @fn SparseString#getFibre
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief Returns a specific fibre of a @link SparseString @endlink.
 * 
 * @signature TFibre getFibre(sparseString, fibreTag);
 * 
 * @param[in] sparseString The sparseString holding the fibre.
 * @param[in] fibreTag A tag that identifies the @link Fibre @endlink. Types:
 *                     @link SparseStringFibres SparseString Fibres @endlink
 * 
 * @return TFibre A reference to the @link Fibre @endlink object.
 * 
 * @fn SparseString#length
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief Returns the number of elements in the @link SparseString @endlink.
 * 
 * @signature TSize length(sparseString);
 * 
 * @param[in] sparseString The sparse string suffix array.
 * 
 * @return TSize The number of elements in the sparse string array. Types: The
 *               result of @link Size @endlink of the sparse string.
 * 
 * @fn SparseString#resize
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief Resets the number of elements in the compressed suffix array.
 * 
 * @note If the new length is smaller than the actual one then the last
 *       <tt>x<tt> items of the compressed suffix array are deleted with <tt>x =
 *       oldLength - newLength</tt>.
 * 
 * @signature TSize resize(sparseString, newLength);
 * 
 * @param[in,out] sparseString The sparse string.
 * @param[in] newLength The number of elements which should be stored in the
 *                      sparse string. Types: @link UnsignedIntegerConcept
 *                      @endlink.
 * 
 * @return TSize The number of elements in the sparse string. Types: The result
 *               of @link Size @endlink of the sparse string.
 * 
 * @fn SparseString#open
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief This functions open a sparse string from disk.
 * 
 * @signature bool open(string, fileName[, openMode]);
 * 
 * @param[in] string The string to be opened. Types: SparseString
 * @param[in] fileName C-style character string containing the file name.
 * @param[in] openMode The combination of flags defining how the file should be
 *                     opened. To open a file read-only, write-only or to read
 *                     and write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>,
 *                     or <tt>OPEN_RDWR</tt>.To create or overwrite a file add
 *                     <tt>OPEN_CREATE</tt>. To append a file if existing add
 *                     <tt>OPEN_APPEND</tt>. To circumvent problems, files are
 *                     always opened in binary mode. Default: <tt>OPEN_RDWR |
 *                     OPEN_CREATE | OPEN_APPEND</tt>
 * 
 * @return bool <tt>true</tt> on success.
 * 
 * @fn SparseString#save
 * 
 * @headerfile <seqan/index.h>
 * 
 * @brief This functions saves a sparse string to disk.
 * 
 * @signature bool save(string, fileName[, openMode]);
 * 
 * @param[in] string The string to be saved. Types: SparseString
 * @param[in] fileName C-style character string containing the file name.
 * @param[in] openMode The combination of flags defining how the file should be
 *                     opened. To open a file read-only, write-only or to read
 *                     and write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>,
 *                     or <tt>OPEN_RDWR</tt>.To create or overwrite a file add
 *                     <tt>OPEN_CREATE</tt>. To append a file if existing add
 *                     <tt>OPEN_APPEND</tt>. To circumvent problems, files are
 *                     always opened in binary mode. Default: <tt>OPEN_RDWR |
 *                     OPEN_CREATE | OPEN_APPEND</tt>
 * 
 * @return bool <tt>true</tt> on success.
 */