IndexQGram - SeqAn API Documentation

# Spec IndexQGram
An index based on an array of sorted q-grams.

Extends | Index
Implements | StringTrieConcept
All Extended | Index
All Subcl's | OpenAddressingQGramIndex
All Impl'd | StringTrieConcept
Defined in | <seqan/index.h>
Signature | `template <typename TIndex, typename TShapeSpec, typename TSpec> class Index<TText, IndexQGram<TShapeSpec[, TSpec]> >;`

## Template Parameters

`TSpec` | The specializing type. Types: OpenAdressing, Default: void
`TText` | The text type. Types: String
`TShapeSpec` | The Shape specialization type.

## Member Function Overview

- `Index::Index();, Index::Index(index);, Index::Index(text[, shape]);`
  Constructor

## Interface Function Overview

- `TSize countOccurrences(index, shape);`
  Returns the number of occurrences of a q-gram in the index text.
- `TCountInfix countOccurrencesMultiple(index, shape);`
  Returns the number of occurrences of a q-gram for every sequence of a StringSet .
- `void createCountsArray(counts, dir, bucketMap, stringSet, shape, stepSize);`
  Builds an index on a StringSet storing how often a q-gram occurs in each sequence.
- `void createQGramIndex(index);, void createQGramIndex(sa, dir, bucketMap, text, shape, stepSize); [DEPRECATED]`
  Builds a q-gram index on a sequence.
- `void createQGramIndexDirOnly(dir, bucketMap, text, shape, stepSize);`
  Builds the directory of a q-gram index on a sequence.
- `void createQGramIndexSAOnly(sa, text, shape, stepSize)`
  Builds the suffix array of a q-gram index on a sequence.
- `TFibre dirAt(position, index);`
  Shortcut for `value(indexDir(index), position)`.
- `void getKmerSimilarityMatrix(index, distMat[, seqSet]);`
  Creates a matrix storing the number of common q-grams between all pairs of sequences.
- `TSAValue getOccurrence(index, shape);`
  Returns an occurrence a q-gram in the index text.
- `TSAInfix getOccurrences(index, shape);`
  Returns all occurrences of a q-gram in the index text.
- `TSize getStepSize(index);`
  Return the q-gram step size used for index creation.
- `TFibre indexBucketMap(index);`
  Shortcut for `getFibre(index, QGramBucketMap())`.
- `TFibre indexCounts(index);`
  Shortcut for `getFibre(index, QGramCounts())`.
- `TFibre indexCountsDir(index);`
  Shortcut for `getFibre(index, QGramCountsDir())`.
- `TFibre indexDir(index);`
  Shortcut for `getFibre(.., QGramDir())`.
- `TSa indexSA(index);`
  Shortcut for `getFibre(.., QGramSA)`.
- `TFibre indexShape(index);`
  Shortcut for `getFibre(index, QGramShape())`.
- `TPair range(index, shape);`
  Returns the suffix array interval borders of a q-gram in the index text.
- `TValue saAt(position, index);`
  Shortcut for `value(indexSA(..), ..)`.
- `void setStepSize(index, stepSize);`
  Change the q-gram step size used for index creation.

### Interface Functions Inherited From Index

- `clear`
- `countSequences`
- `getFibre`
- `indexCreate`
- `indexRawText`
- `indexRequire`
- `indexSupplied`
- `indexText`
- `length`
- `open`
- `rawtextAt`
- `save`

## Interface Metafunction Overview

### Interface Metafunctions Inherited From Index

- `DefaultIndexCreator`
- `DefaultIndexSpec`
- `DefaultIndexStringSpec`
- `GetVSTreeIteratorTraits`
- `Size`

## Detailed Description

The fibres (see Index and Fibre) of this index are a suffix array sorted by the first q characters (see QGramSA) and a q-gram directory (see QGramDir).

The size of the q-gram directory is Σq. On a 32 bit system the q-gram length is limited to 3 for `char` alphabets or 13-14 for Dna alphabets.

Consider to use the OpenAddressingQGramIndex for longer q-grams if you don't need q-grams to be sorted.

## See Also

- QGramIndexFibres

## Member Functions Detail

### `Index::Index(); Index::Index(index); Index::Index(text[, shape]);`

Constructor

#### Parameters

`index` | Other Index object to copy from.
`text` | The text to be indexed.
`shape` | The q gram Shape to be applied. (optional)

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

## Interface Functions Detail

### `TSize countOccurrences(index, shape);`

Returns the number of occurrences of a q-gram in the index text.

#### Parameters

`index` | IndexQGram object to query.
`shape` | A Shape object to use for the query.

#### Returns

`TSize` | The number of positions where the q-gram stored in `shape` occurs in the text (see QGramText). Metafunction: Size.

The necessary index tables are built on-demand via indexRequire if index is not `const`.

Demo: Demo.Supermaximal Repeats

Demo: Demo.Index countChildren

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TCountInfix countOccurrencesMultiple(index, shape);`

Returns the number of occurrences of a q-gram for every sequence of a StringSet .

#### Parameters

`index` | A IndexQGram of a StringSet.
`shape` | A Shape.

#### Returns

`TCountInfix` | A sequence of pairs (seqNo,count), count > 0. For every StringSet sequence the q-gram occurs in, seqNo is the sequence number and count the number of occurrences. If the type of `index` is `TIndex` the return type is `Infix<Fibre<TIndex, QGramCounts>::Type const>::Type`.

The necessary index tables are built on-demand via indexRequire if index is not `const`.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

#### See Also

- countOccurrences

### `void createCountsArray(counts, dir, bucketMap, stringSet, shape, stepSize);`

Warning.

This function should not be called directly. Please use indexCreate or indexRequire. The resulting tables must have appropriate size before calling this function.

Builds an index on a StringSet storing how often a q-gram occurs in each sequence.

#### Parameters

`counts` | The resulting String of pairs (seqNo, count).
`dir` | The resulting array that indicates at which position in the count table the corresponding a certain q-gram can be found.
`bucketMap` | Stores the q-gram hashes for the openaddressing hash maps, see indexBucketMap. If bucketMap is of the type Nothing the q-gram hash determines the bucket address in the index.
`stringSet` | The StringSet.
`shape` | The Shape to be used.
`stepSize` | Store every `stepSize`th q-gram in the index, IntegerConcept.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void createQGramIndex(index); void createQGramIndex(sa, dir, bucketMap, text, shape, stepSize); [DEPRECATED]`

Warning.

This function should not be called directly. Please use indexCreate or indexRequire. The resulting tables must have appropriate size before calling this function.

Builds a q-gram index on a sequence.

#### Parameters

`index` | The IndexQGram to create.
`sa` | The resulting list in which all q-grams are sorted alphabetically.
`dir` | The resulting array that indicates at which position in index the corresponding q-grams
`bucketMap` | Stores the q-gram hashes for the openaddressing hash maps, see indexBucketMap. If bucketMap is of the type Nothing the q-gram hash determines the bucket address in the index.
`text` | The TextConcept object to build the index for.
`shape` | The shape to be used. Types: Shape can be found.
`stepSize` | Store every `stepSize`'th q-gram in the index, IntegerConcept.

The resulting q-gram `index` contains the sorted list of qgrams. For each q-gram `dir` contains the first position in index that corresponds to this q-gram.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void createQGramIndexDirOnly(dir, bucketMap, text, shape, stepSize);`

Warning.

This function should not be called directly. Please use indexCreate or indexRequire. The resulting tables must have appropriate size before calling this function.

Builds the directory of a q-gram index on a sequence.

#### Parameters

`dir` | The resulting array that indicates at which position in index the corresponding q-grams can be found.
`bucketMap` | Stores the q-gram hashes for the openaddressing hash maps, see indexBucketMap. If bucketMap is of the type Nothing the q-gram hash determines the bucket address in the index.
`text` | The sequence, TextConcept.
`stepSize` | Store every `stepSize`'th q-gram in the index, IntegerConcept.
`shape` | The Shape to be used.

The resulting `index` contains the sorted list of qgrams. For each possible q-gram pos contains the first position in index that corresponds to this q-gram.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void createQGramIndexSAOnly(sa, text, shape, stepSize)`

Warning.

This function should not be called directly. Please use indexCreate or indexRequire. The resulting tables must have appropriate size before calling this function.

Builds the suffix array of a q-gram index on a sequence.

#### Parameters

`sa` | The resulting list in which all q-grams are sorted alphabetically, String object of SAValue of the underlying text.
`text` | The sequence, a TextConcept object.
`shape` | The Shape to be used. q is the length of this shape.
`stepSize` | Store every `stepSize`'th q-gram in the index, IntegerConcept.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TFibre dirAt(position, index);`

Shortcut for `value(indexDir(index), position)`.

#### Parameters

`index` | The IndexQGram object holding the fibre.
`position` | A position in the array on which the value should be accessed.

#### Returns

`TFibre` | A reference to the QGramDir fibre.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void getKmerSimilarityMatrix(index, distMat[, seqSet]);`

Creates a matrix storing the number of common q-grams between all pairs of sequences.

#### Parameters

`distMat` | The resulting q-gram similarity matrix. Types: ContainerConcept
`seqSet` | Contains sequence numbers if only a subset of sequences should be compared. Types: ContainerConcept
`index` | The IndexQGram to use.

`distMat` need to be a container of a floating point type and will be resized to `seqCount * seqCount`, where `seqCount` is the number of sequences in the index/in `seqSet`. The fraction of common q-grams between sequence `i` and `j` is stored at position `i*seqCount + j`. It sums up the minimum number of q-gram occurrences between both sequences for each q-gram and normalizes it.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TSAValue getOccurrence(index, shape);`

Returns an occurrence a q-gram in the index text.

#### Parameters

`index` | The IndexQGram object to query.
`shape` | The Shape object to use for the query. The shape stores the q-gram of the last call ot hash or hashNext.

#### Returns

`TSAValue` | A position where the q-gram stored in `shape` occurs in the text (see QGramText). Type: SAValue of the index type.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TSAInfix getOccurrences(index, shape);`

Returns all occurrences of a q-gram in the index text.

#### Parameters

`index` | A IndexQGram to query.
`shape` | A Shape object.

#### Returns

`TSAInfix` | All positions where the q-gram stored in `shape` occurs in the text (see QGramText). Tupes: Infix<Fibre<TIndex, QGramSA>::Type>::Type>.

The necessary index tables are built on-demand via indexRequire if index is not `const`.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

#### See Also

- DemoMaximalUniqueMatches
- DemoMummy
- DemoSupermaximalRepeats
- getFrequency
- isLeftMaximal
- isPartiallyLeftExtensible
- isUnique

### `TSize getStepSize(index);`

Return the q-gram step size used for index creation.

#### Parameters

`index` | A IndexQGram object.

#### Returns

`TSize` | The step size of type Size. If x is returned every xth q-gram is stored in the index.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

#### See Also

- setStepSize

### `TFibre indexBucketMap(index);`

Shortcut for `getFibre(index, QGramBucketMap())`.

#### Parameters

`index` | The IndexQGram object holding the fibre.

#### Returns

`TFibre` | A reference to the QGramBucketMap fibre (maps q-gram hashes to buckets).

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TFibre indexCounts(index);`

Shortcut for `getFibre(index, QGramCounts())`.

#### Parameters

`index` | The IndexQGram object holding the fibre.

#### Returns

`TFibre` | A reference to the QGramCounts fibre (counts array).

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TFibre indexCountsDir(index);`

Shortcut for `getFibre(index, QGramCountsDir())`.

#### Parameters

`index` | The IndexQGram object holding the fibre.

#### Returns

`TFibre` | A reference to the QGramCountsDir fibre (counts directory).

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TFibre indexDir(index);`

Shortcut for `getFibre(.., QGramDir())`.

#### Parameters

`index` | The IndexQGram object holding the fibre.

#### Returns

`TFibre` | A reference to the QGramDir fibre (q-gram directory).

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TSa indexSA(index);`

Shortcut for `getFibre(.., QGramSA)`.

#### Parameters

`index` | The IndexQGram object holding the fibre.

#### Returns

`TSa` | A reference to the QGramSA fibre (q-gram positions).

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TFibre indexShape(index);`

Shortcut for `getFibre(index, QGramShape())`.

#### Parameters

`index` | The Index object holding the fibre. Types: IndexQGram

#### Returns

`TFibre` | Returns a reference to the Shape object of a q-gram index. Formally, this is a reference to the QGramShape fibre.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TPair range(index, shape);`

Returns the suffix array interval borders of a q-gram in the index text.

#### Parameters

`index` | The IndexQGram object to query.
`shape` | The Shape object to use for the query.

#### Returns

`TPair` | All positions where the q-gram stored in `shape` occurs in the text (see QGramText) are stored in a contiguous range of the suffix array. `range` returns begin and end position of this range. If the type of `index` is `TIndex` the return type is `Pair<Size<TIndex>::Type>`.

The necessary index tables are built on-demand via indexRequire if index is not `const`.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TValue saAt(position, index);`

Note.

Advanced functionality, not commonly used.

Shortcut for `value(indexSA(..), ..)`.

#### Parameters

`index` | The IndexQGram object holding the fibre.
`position` | A position in the array on which the value should be accessed.

#### Returns

`TValue` | A reference or proxy to the value in the QGramSA fibre. To be more precise, a reference to a position containing a value of type SAValue is returned (or a proxy).

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void setStepSize(index, stepSize);`

Change the q-gram step size used for index creation.

#### Parameters

`index` | The IndexQGram to modify.
`stepSize` | The step size, IntegerConcept; Each `stepSize`th q-gram will be stored.

The default step size of a q-gram index is 1, which corresponds to all overlapping q-grams. To take effect of changing the `stepSize` the q-gram index should be empty or recreated.

A `stepSize` of 0 corresponds to `stepSize = length(indexShape(index))`, i.e. all non-overlapping q-grams.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

#### See Also

- getStepSize

#### Dox Sources

    /*!
     * @class IndexQGram
     *
     * @implements StringTrieConcept
     *
     * @extends Index
     *
     * @headerfile <seqan/index.h>
     *
     * @brief An index based on an array of sorted q-grams.
     *
     * @signature template <typename TIndex, typename TShapeSpec, typename TSpec>
     *            class Index<TText, IndexQGram<TShapeSpec[, TSpec]> >;
     *
     * @tparam TSpec The specializing type. Types: @link
     *               OpenAdressingTags#OpenAdressing @endlink, Default: void
     * @tparam TText The text type. Types: @link String @endlink
     * @tparam TShapeSpec The @link Shape @endlink specialization type.
     *
     * The fibres (see @link Index @endlink and @link Fibre @endlink) of this index
     * are a suffix array sorted by the first <i>q</i> characters (see @link
     * QGramIndexFibres#QGramSA @endlink) and a <i>q</i>-gram directory (see @link
     * QGramIndexFibres#QGramDir @endlink).
     *
     * The size of the q-gram directory is <i>&Sigma;<sup>q</sup></i>. On a 32 bit
     * system the <i>q</i>-gram length is limited to 3 for <tt>char</tt> alphabets
     * or 13-14 for @link Dna @endlink alphabets.
     *
     * Consider to use the @link OpenAddressingQGramIndex @endlink for longer
     * <i>q</i>-grams if you don't need <i>q</i>-grams to be sorted.
     *
     * @see QGramIndexFibres
     *
     * @fn IndexQGram::Index
     *
     * @brief Constructor
     *
     * @signature Index::Index();
     * @signature Index::Index(index);
     * @signature Index::Index(text[, shape]);
     *
     * @param[in] index Other Index object to copy from.
     * @param[in] text The text to be indexed.
     * @param[in] shape The q gram @link Shape @endlink to be applied. (optional)
     *
     * @fn IndexQGram#indexSA
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Shortcut for <tt>getFibre(.., QGramSA)</tt>.
     *
     * @signature TSa indexSA(index);
     *
     * @param[in] index The @link IndexQGram @endlink object holding the fibre.
     *
     * @return TSa A reference to the @link QGramIndexFibres#QGramSA @endlink fibre
     *             (q-gram positions).
     *
     * @fn IndexQGram#saAt
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Shortcut for <tt>value(indexSA(..), ..)</tt>.
     *
     * @note Advanced functionality, not commonly used.
     *
     * @signature TValue saAt(position, index);
     *
     * @param[in] index The @link IndexQGram @endlink object holding the fibre.
     * @param[in] position A position in the array on which the value should be
     *                     accessed.
     *
     * @return TValue A reference or proxy to the value in the @link
     *                QGramIndexFibres#QGramSA @endlink fibre. To be more precise, a
     *                reference to a position containing a value of type @link
     *                SAValue @endlink is returned (or a proxy).
     *
     * @fn IndexQGram#indexDir
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Shortcut for <tt>getFibre(.., QGramDir())</tt>.
     *
     * @signature TFibre indexDir(index);
     *
     * @param[in] index The @link IndexQGram @endlink object holding the fibre.
     *
     * @return TFibre A reference to the @link QGramIndexFibres#QGramDir @endlink
     *                fibre (q-gram directory).
     *
     * @fn IndexQGram#dirAt
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Shortcut for <tt>value(indexDir(index), position)</tt>.
     *
     * @signature TFibre dirAt(position, index);
     *
     * @param[in] index The IndexQGram object holding the fibre.
     * @param[in] position A position in the array on which the value should be
     *                     accessed.
     *
     * @return TFibre A reference to the @link QGramIndexFibres#QGramDir @endlink
     *                fibre.
     *
     * @fn IndexQGram#indexCounts
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Shortcut for <tt>getFibre(index, QGramCounts())</tt>.
     *
     * @signature TFibre indexCounts(index);
     *
     * @param[in] index The @link IndexQGram @endlink object holding the fibre.
     *
     * @return TFibre A reference to the @link QGramIndexFibres#QGramCounts @endlink
     *                fibre (counts array).
     *
     * @fn IndexQGram#indexCountsDir
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Shortcut for <tt>getFibre(index, QGramCountsDir())</tt>.
     *
     * @signature TFibre indexCountsDir(index);
     *
     * @param[in] index The IndexQGram object holding the fibre.
     *
     * @return TFibre A reference to the @link QGramIndexFibres#QGramCountsDir
     *                @endlink fibre (counts directory).
     *
     * @fn IndexQGram#indexBucketMap
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Shortcut for <tt>getFibre(index, QGramBucketMap())</tt>.
     *
     * @signature TFibre indexBucketMap(index);
     *
     * @param[in] index The IndexQGram object holding the fibre.
     *
     * @return TFibre A reference to the @link QGramIndexFibres#QGramBucketMap
     *                @endlink fibre (maps q-gram hashes to buckets).
     *
     * @fn IndexQGram#indexShape
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Shortcut for <tt>getFibre(index, QGramShape())</tt>.
     *
     * @signature TFibre indexShape(index);
     *
     * @param[in] index The @link Index @endlink object holding the fibre. Types:
     *                  @link IndexQGram @endlink
     *
     * @return TFibre Returns a reference to the @link Shape @endlink object of a
     *                q-gram index. Formally, this is a reference to the @link
     *                QGramIndexFibres#QGramShape @endlink fibre.
     *
     * @fn IndexQGram#getStepSize
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Return the <i>q</i>-gram step size used for index creation.
     *
     * @signature TSize getStepSize(index);
     *
     * @param[in] index A IndexQGram object.
     *
     * @return TSize The step size of type @link Index#Size @endlink. If <i>x</i> is
     *               returned every <i>x</i><sup>th</sup> <i>q</i>-gram is stored in
     *               the index.
     *
     * @see IndexQGram#setStepSize
     *
     * @fn IndexQGram#setStepSize
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Change the <i>q</i>-gram step size used for index creation.
     *
     * @signature void setStepSize(index, stepSize);
     *
     * @param[in,out] index The IndexQGram to modify.
     * @param[in] stepSize The step size, @link IntegerConcept @endlink; Each
     *                     <tt>stepSize</tt><sup>th</sup> <i>q</i>-gram will be
     *                     stored.
     *
     * The default step size of a <i>q</i>-gram index is 1, which corresponds to all
     * overlapping <i>q</i>-grams. To take effect of changing the <tt>stepSize</tt>
     * the <i>q</i>-gram index should be empty or recreated.
     *
     * A <tt>stepSize</tt> of 0 corresponds to <tt>stepSize =
     * length(indexShape(index))</tt>, i.e. all non-overlapping q-grams.
     *
     * @see IndexQGram#getStepSize
     *
     * @fn IndexQGram#createQGramIndex
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Builds a <i>q</i>-gram index on a sequence.
     *
     * @warning This function should not be called directly. Please use @link
     *          Index#indexCreate @endlink or @link Index#indexRequire @endlink. The
     *          resulting tables must have appropriate size before calling this
     *          function.
     *
     * @signature void createQGramIndex(index);
     * @signature void createQGramIndex(sa, dir, bucketMap, text, shape, stepSize);
     *            [DEPRECATED]
     *
     * @param[out] index The IndexQGram to create.
     * @param[out] sa The resulting list in which all <i>q</i>-grams are sorted
     *                alphabetically.
     * @param[out] dir The resulting array that indicates at which position in index
     *                 the corresponding <i>q</i>-grams
     * @param[in] bucketMap Stores the <i>q</i>-gram hashes for the openaddressing
     *                      hash maps, see @link IndexQGram#indexBucketMap @endlink.
     *                      If bucketMap is of the type @link Nothing @endlink the
     *                      <i>q</i>-gram hash determines the bucket address in the
     *                      index.
     * @param[in] text The @link TextConcept @endlink object to build the index for.
     * @param[in] shape The shape to be used. Types: @link Shape @endlink can be
     *                  found.
     * @param[in] stepSize Store every <tt>stepSize</tt>'th <i>q</i>-gram in the
     *                     index, @link IntegerConcept @endlink.
     *
     * The resulting <i>q</i>-gram <tt>index</tt> contains the sorted list of
     * qgrams. For each <i>q</i>-gram <tt>dir</tt> contains the first position in
     * index that corresponds to this <i>q</i>-gram.
     *
     * @fn IndexQGram#createQGramIndexSAOnly
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Builds the suffix array of a q-gram index on a sequence.
     *
     * @warning This function should not be called directly. Please use @link
     *          Index#indexCreate @endlink or @link Index#indexRequire @endlink. The
     *          resulting tables must have appropriate size before calling this
     *          function.
     *
     * @signature void createQGramIndexSAOnly(sa, text, shape, stepSize)
     *
     * @param[out] sa The resulting list in which all q-grams are sorted
     *                alphabetically, @link String @endlink object of @link SAValue
     *                @endlink of the underlying @link TextConcept text @endlink.
     * @param[in] text The sequence, a @link TextConcept @endlink object.
     * @param[in] shape The @link Shape @endlink to be used. q is the length of this
     *                  shape.
     * @param[in] stepSize Store every <tt>stepSize</tt>'th q-gram in the index,
     *                     @link IntegerConcept @endlink.
     *
     * @fn IndexQGram#createQGramIndexDirOnly
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Builds the directory of a <i>q</i>-gram index on a sequence.
     *
     * @warning This function should not be called directly. Please use @link
     *          Index#indexCreate @endlink or @link Index#indexRequire @endlink. The
     *          resulting tables must have appropriate size before calling this
     *          function.
     *
     * @signature void createQGramIndexDirOnly(dir, bucketMap, text, shape,
     *            stepSize);
     *
     * @param[out] dir The resulting array that indicates at which position in index
     *                 the corresponding q-grams can be found.
     * @param[out] bucketMap Stores the q-gram hashes for the openaddressing hash
     *                       maps, see @link IndexQGram#indexBucketMap @endlink. If
     *                       bucketMap is of the type @link Nothing @endlink the
     *                       q-gram hash determines the bucket address in the index.
     * @param[in] text The sequence, @link TextConcept @endlink.
     * @param[in] stepSize Store every <tt>stepSize</tt>'th q-gram in the index,
     *                     @link IntegerConcept @endlink.
     * @param[in] shape The @link Shape @endlink to be used.
     *
     * The resulting <tt>index</tt> contains the sorted list of qgrams. For each
     * possible q-gram pos contains the first position in index that corresponds to
     * this q-gram.
     *
     * @fn IndexQGram#createCountArray
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Builds an index on a StringSet storing how often a <i>q</i>-gram
     *        occurs in each sequence.
     *
     * @warning This function should not be called directly. Please use @link
     *          Index#indexCreate @endlink or @link Index#indexRequire @endlink. The
     *          resulting tables must have appropriate size before calling this
     *          function.
     *
     * @signature void createCountsArray(counts, dir, bucketMap, stringSet, shape,
     *            stepSize);
     *
     * @param[out] counts The resulting @link String @endlink of pairs <i>(seqNo,
     *                    count)</i>.
     * @param[out] dir The resulting array that indicates at which position in the
     *                 count table the corresponding a certain q-gram can be found.
     * @param[out] bucketMap Stores the q-gram hashes for the openaddressing hash
     *                       maps, see @link IndexQGram#indexBucketMap @endlink. If
     *                       bucketMap is of the type @link Nothing @endlink the
     *                       q-gram hash determines the bucket address in the index.
     * @param[in] stringSet The @link StringSet @endlink.
     * @param[in] shape The @link Shape @endlink to be used.
     * @param[in] stepSize Store every <tt>stepSize</tt><sup>th</sup> <i>q</i>-gram
     *                     in the index, @link IntegerConcept @endlink.
     *
     * @fn IndexQGram#getKmerSimilarityMatrix
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Creates a matrix storing the number of common q-grams between all
     *        pairs of sequences.
     *
     * @signature void getKmerSimilarityMatrix(index, distMat[, seqSet]);
     *
     * @param[out] distMat The resulting q-gram similarity matrix. Types: @link
     *                     ContainerConcept @endlink
     * @param[in] seqSet Contains sequence numbers if only a subset of sequences
     *                   should be compared. Types: @link ContainerConcept @endlink
     * @param[in] index The @link IndexQGram @endlink to use.
     *
     * <tt>distMat</tt> need to be a container of a floating point type and will be
     * resized to <tt>seqCount * seqCount</tt>, where <tt>seqCount</tt> is the
     * number of sequences in the index/in <tt>seqSet</tt>. The fraction of common
     * q-grams between sequence <tt>i</tt> and <tt>j</tt> is stored at position
     * <tt>i*seqCount + j</tt>. It sums up the minimum number of q-gram occurrences
     * between both sequences for each q-gram and normalizes it.
     *
     * @fn IndexQGram#range
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns the suffix array interval borders of a q-gram in the index
     *        text.
     *
     * @signature TPair range(index, shape);
     *
     * @param[in] index The IndexQGram object to query.
     * @param[in] shape The @link Shape @endlink object to use for the query.
     *
     * @return TPair All positions where the q-gram stored in <tt>shape</tt> occurs
     *               in the text (see @link QGramIndexFibres#QGramText @endlink) are
     *               stored in a contiguous range of the suffix array.
     *               <tt>range</tt> returns begin and end position of this range. If
     *               the type of <tt>index</tt> is <tt>TIndex</tt> the return type
     *               is <tt>Pair&lt;Size&lt;TIndex&gt;::Type&gt;</tt>.
     *
     * The necessary index tables are built on-demand via @link Index#indexRequire
     * @endlink if index is not <tt>const</tt>.
     *
     * @fn IndexQGram#getOccurrence
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns an occurrence a q-gram in the index text.
     *
     * @signature TSAValue getOccurrence(index, shape);
     *
     * @param[in] index The IndexQGram object to query.
     * @param[in] shape The @link Shape @endlink object to use for the query. The
     *                  shape stores the <i>q</i>-gram of the last call ot @link
     *                  Shape#hash @endlink or @link Shape#hashNext @endlink.
     *
     * @return TSAValue A position where the <i>q</i>-gram stored in <tt>shape</tt>
     *                  occurs in the text (see @link QGramIndexFibres#QGramText
     *                  @endlink). Type: @link SAValue @endlink of the index type.
     *
     * @fn IndexQGram#getOccurrences
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns all occurrences of a q-gram in the index text.
     *
     * @signature TSAInfix getOccurrences(index, shape);
     *
     * @param[in] index A IndexQGram to query.
     * @param[in] shape A @link Shape @endlink object.
     *
     * @return TSAInfix All positions where the q-gram stored in <tt>shape</tt>
     *                  occurs in the text (see @link QGramIndexFibres#QGramText
     *                  @endlink). Tupes: @link SegmentableConcept#Infix
     *                  @endlink<@link Fibre @endlink<TIndex,
     *                  QGramSA>::Type>::Type>.
     *
     * The necessary index tables are built on-demand via @link Index#indexRequire
     * @endlink if index is not <tt>const</tt>.
     *
     * @see DemoMummy
     * @see DemoSupermaximalRepeats
     * @see DemoMaximalUniqueMatches
     * @see VSTreeIterator#isUnique
     * @see VSTreeIterator#getFrequency
     * @see VSTreeIterator#isPartiallyLeftExtensible
     * @see VSTreeIterator#isLeftMaximal
     *
     * @fn IndexQGram#countOccurrences
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns the number of occurrences of a q-gram in the index text.
     *
     * @signature TSize countOccurrences(index, shape);
     *
     * @param[in] index IndexQGram object to query.
     * @param[in] shape A @link Shape @endlink object to use for the query.
     *
     * @return TSize The number of positions where the q-gram stored in
     *               <tt>shape</tt> occurs in the text (see @link
     *               QGramIndexFibres#QGramText @endlink). Metafunction: @link
     *               Index#Size @endlink.
     *
     * The necessary index tables are built on-demand via @link Index#indexRequire
     * @endlink if index is not <tt>const</tt>.
     *
     * Demo: Demo.Supermaximal Repeats
     *
     * Demo: Demo.Index countChildren
     *
     * @fn IndexQGram#countOccurrencesMultiple
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns the number of occurrences of a q-gram for every sequence of a
     *        @link StringSet @endlink .
     *
     * @signature TCountInfix countOccurrencesMultiple(index, shape);
     *
     * @param[in] index A IndexQGram of a @link StringSet @endlink.
     * @param[in] shape A @link Shape @endlink.
     *
     * @return TCountInfix A sequence of @link Pair pairs @endlink (seqNo,count),
     *                     count &gt; 0. For every @link StringSet @endlink sequence
     *                     the q-gram occurs in, seqNo is the sequence number and
     *                     count the number of occurrences. If the type of
     *                     <tt>index</tt> is <tt>TIndex</tt> the return type is
     *                     <tt>Infix&lt;Fibre&lt;TIndex, QGramCounts&gt;::Type
     *                     const&gt;::Type</tt>.
     *
     * The necessary index tables are built on-demand via @link Index#indexRequire
     * @endlink if index is not <tt>const</tt>.
     *
     * @see VSTreeIterator#countOccurrences
     */